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Description
I don't claim anatomical accuracy in any way, this is just a sketch to show the general arrangement of the organs and how the skeleton looks like in my reconstruction of the internal systems of a Centaur. I cut the organs and the bones where necessary, but I hope the overall design is clear.
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My hypothesis stems from the origin I chose for the Centaurs: in ancient times they appeared on earth as spirits of the wind in the Mongolian steppes, and then started to take the shape of a man combined with a horse… as the time passed, this spirits started to became always more physical, and as the two systems biologically developed to cope one with the other, magic supported the entire organism until the whole thing worked. So, what I’m saying is that basically the Centaurs started as creatures with 2 sets of all organs, two lungs, two digestive systems, two hearts etc. but as the time passed and biology started to take over the magical aspects, the binary systems progressively organized to fit the task of keeping the Centaur alive and started to work as a single system: some of the organs shrink or atrophied, while some others enlarged and turned hypertrophied. For example, it’s impossible to make two sets of lungs work properly for a mammalian respiratory system, so the second pair simply disappeared, while the first pair enlarged and developed many methods to cope with the relative small amount of oxygen they can intake (we’ll see that later). On the contrary, a second heart is required to keep the extremities vital, so even if the upper heart enlarged (it was preferred due to its proximity to the brain), the lower one shrank but persisted, and a large nervous ganglion (a la stegosaurus) evolved to assist in the complex task of synchronize the beat of the two hearts. So basically the upper torso specialized to host the respiratory and circulatory system by extending abnormally the ribcage and filling the space left in the torso with the right organs, while the lower torso specialized with the digestive and excretory system, made bigger because the Centaur has to eat a lot and absorb a vast quantity of nutrients to keep its organism efficient (in few words: everything is bigger in the Centaur.)

The main facts are written in the picture, but here are some minor details:

Lungs work through a combination of sheer power of the diaphragm (this means that Centaurs take extremely long and deep breaths) and biochemical adaptations: like in moles and other mammals which have to cope with oxygen problems, Centaurs have an increased capability of absorb oxygen and tolerate its absence. Besides, there is also another clever trick they developed: in nature, there is only one type of creature which have to breath for two and share its circulatory system with another creature to which is fused, and that is a mother: we don’t think to it often but a mother is two creature in one, and has to do all the tasks which she used to do for one being, to sustain two lives. How does she do that? It’s simple: in mammals the fetus has a blood composition slightly different from that of an adult, with a special kind of hemoglobin which is far better in binding oxygen. Centaurs retained this kind of hemoglobin in adulthood too.

The skull reflects the respiration habits of the Centaurs… the nasal opening is greatly enlarged and is sustained by a bony protrusion (which gives to the Centaur a characteristic "Greek nose"), but to grant a sufficient amount of air intake, the Centaur often has to breath with its mouth too. This leads to a series of bone modifications which in humans are note as Long Face Syndrome, which contributes to make the face of the Centaur look superficially similar to that of a horse, although the Centaur body is designed to cope with the modifications, so that they don’t have drawbacks from the “syndrome”, and the overall aspect is neat and shapely. A Centaur’s brain is bigger than ours, but a large part of it consists in a large cerebellum which coordinates the six limbs, so the occipital bone is bigger and the entire skull extends backwards. The mouth can be opened more than that of a human (the Centaur has to eat a lot, remember?) and powerful muscles assist mastication.

Speaking of eating, the Centaur’s diet is essentially made up by game and a lot of proteins, as they originated as prairie hunters: although it is placed in the horse half, the digestive system is very “human”. Horse has a relatively small stomach, while Centaurs has a very big one: besides, they have a caecum, which they use to integrate their diet with vegetables and various kinds of herbs. They easily get drunk, but this is not due to their inability to vomit, because in fact they can. Instead, the inebriation is induced by the absence of enzymes which metabolize alcohol: this activates the liver and thus diverts the blood from the primary brain to the digestive coordination ganglion, unleashing inhibitions and inducing euphoria more than usual. They have a taste for everything sweet, and that’s why they used to love wine in ancient times, because it was mixed with honey. Also, they have a low metabolism.
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In encourage you to ask questions

Description
I don't claim anatomical accuracy in any way, this is just a sketch to show the general arrangement of the organs and how the skeleton looks like in my reconstruction of the internal systems of a Centaur. I cut the organs and the bones where necessary, but I hope the overall design is clear.
---
My hypothesis stems from the origin I chose for the Centaurs: in ancient times they appeared on earth as spirits of the wind in the Mongolian steppes, and then started to take the shape of a man combined with a horse… as the time passed, this spirits started to became always more physical, and as the two systems biologically developed to cope one with the other, magic supported the entire organism until the whole thing worked. So, what I’m saying is that basically the Centaurs started as creatures with 2 sets of all organs, two lungs, two digestive systems, two hearts etc. but as the time passed and biology started to take over the magical aspects, the binary systems progressively organized to fit the task of keeping the Centaur alive and started to work as a single system: some of the organs shrink or atrophied, while some others enlarged and turned hypertrophied. For example, it’s impossible to make two sets of lungs work properly for a mammalian respiratory system, so the second pair simply disappeared, while the first pair enlarged and developed many methods to cope with the relative small amount of oxygen they can intake (we’ll see that later). On the contrary, a second heart is required to keep the extremities vital, so even if the upper heart enlarged (it was preferred due to its proximity to the brain), the lower one shrank but persisted, and a large nervous ganglion (a la stegosaurus) evolved to assist in the complex task of synchronize the beat of the two hearts. So basically the upper torso specialized to host the respiratory and circulatory system by extending abnormally the ribcage and filling the space left in the torso with the right organs, while the lower torso specialized with the digestive and excretory system, made bigger because the Centaur has to eat a lot and absorb a vast quantity of nutrients to keep its organism efficient (in few words: everything is bigger in the Centaur.)

The main facts are written in the picture, but here are some minor details:

Lungs work through a combination of sheer power of the diaphragm (this means that Centaurs take extremely long and deep breaths) and biochemical adaptations: like in moles and other mammals which have to cope with oxygen problems, Centaurs have an increased capability of absorb oxygen and tolerate its absence. Besides, there is also another clever trick they developed: in nature, there is only one type of creature which have to breath for two and share its circulatory system with another creature to which is fused, and that is a mother: we don’t think to it often but a mother is two creature in one, and has to do all the tasks which she used to do for one being, to sustain two lives. How does she do that? It’s simple: in mammals the fetus has a blood composition slightly different from that of an adult, with a special kind of hemoglobin which is far better in binding oxygen. Centaurs retained this kind of hemoglobin in adulthood too.

The skull reflects the respiration habits of the Centaurs… the nasal opening is greatly enlarged and is sustained by a bony protrusion (which gives to the Centaur a characteristic "Greek nose"), but to grant a sufficient amount of air intake, the Centaur often has to breath with its mouth too. This leads to a series of bone modifications which in humans are note as Long Face Syndrome, which contributes to make the face of the Centaur look superficially similar to that of a horse, although the Centaur body is designed to cope with the modifications, so that they don’t have drawbacks from the “syndrome”, and the overall aspect is neat and shapely. A Centaur’s brain is bigger than ours, but a large part of it consists in a large cerebellum which coordinates the six limbs, so the occipital bone is bigger and the entire skull extends backwards. The mouth can be opened more than that of a human (the Centaur has to eat a lot, remember?) and powerful muscles assist mastication.

Speaking of eating, the Centaur’s diet is essentially made up by game and a lot of proteins, as they originated as prairie hunters: although it is placed in the horse half, the digestive system is very “human”. Horse has a relatively small stomach, while Centaurs has a very big one: besides, they have a caecum, which they use to integrate their diet with vegetables and various kinds of herbs. They easily get drunk, but this is not due to their inability to vomit, because in fact they can. Instead, the inebriation is induced by the absence of enzymes which metabolize alcohol: this activates the liver and thus diverts the blood from the primary brain to the digestive coordination ganglion, unleashing inhibitions and inducing euphoria more than usual. They have a taste for everything sweet, and that’s why they used to love wine in ancient times, because it was mixed with honey. Also, they have a low metabolism.
---
In encourage you to ask questions