The health standards of amphibians and reptiles should not be judged only based on the presence of obvious pathological manifestations, and those animals that do not show obvious diseases should also be given sufficient attention. The microbiome, in turn, is closely related to the health of amphibians and reptiles. Therefore, in our study, the weight of young alligators at the same age was used as the health indicator of Chinese alligators, and the relationship between the microbiome and the health of young alligators was explored by analyzing the cloacal microbiome of Chinese alligators.