Hupehsuchus was similar to its close cousin, Nanchangosaurus, but differed from it in a number of ways. For example, Hupehsuchus had heavier armor on its back than Nanchangosaurus, and its back spines were more finely divided, giving it a more crocodile-like appearance than Nanchangosaurus. It had a thin, long snout like a gharial, river dolphin, or ichthyosaur, which it probably used to snag fish or probe for aquatic invertebrates.
It is unknown exactly what Hupehsuchus is related to. It is fairly clear that it shares a close relationship with Nanchangosaurus, but other relations are unknown. Many features, including the discovery of polydactyly, suggest that Hupehsuchus is related to the ichthyosaurs, but the fact that Hupehsuchus's extra digits include more bones in the hand, rather than just the fingers as in the ichthyosaurs, may discredit that theory. It along with Nanchangosaurus seem to be so different from any other reptile that a new order has been constructed for the two genera called Hupehsuchia.