Human activities lead to ecosystem fragmentation, accelerated degradation, and permanent decline of biodiversity. Artificial captive breeding is considered an important method for effectively protecting threatened species and is one of the key ways to save endangered animals. However, due to various factors such as food and living environment, animals have undergone significant changes from the wild to the captive environment, leading to a series of problems such as gastrointestinal disorders, infections, and diseases in mammals. The gut microbiota is widely recognized to play a crucial role in maintaining the health of the body, and its disruption and ecological imbalance can directly affect the host’s health. There are many different environmental factors between captive environment and wild environment. This paper discusses the effects of diet change, habitat homogenization, stress and antibiotics on gut microbiota of wild mammals in captivity. The diversity of gut microorganisms of different feeding mammals did not change uniformly, but their composition and structure all changed when they were faced with the simplification of the captive diet. The high homogeneity of the habitats in captivity made the gut microorganisms of mammals show different degrees of humanization. Various stresses in captivity can cause imbalances in mammalian gut microbiota. Direct or indirect use of antibiotics in captivity can alter the composition of mammalian gut microbiota and increase the variety and number of antibiotic resistance genes in gut microbiota. These changes have altered the gut microbiota and impacted the health of captive wild mammals, affecting wildlife reintroduction efforts. Future research direction is also discussed in order to provide guidelines for the protection of wild mammals.