The gut microbiome is the second set of animal genomes and interacts with hosts in development, nutrition metabolism, physiological function, and immunity. Non-human primates (NHPs) are close to humans in terms of ecological niche, social structure, geographical distribution and evolution. The research of NHPs gut microbiome not only contributes to understanding primate ecology, conservation, and evolution but has also important reference value for in-depth understanding of the role of the gut microbiome in human evolution. This paper summarizes the factors influencing the composition of the gut microbiome in NHPs, including host species and phylogeny, diet, habitat fragmentation, age/sex, captivity, and community life. We also explore the application of gut microbiome research in NHPs ecology, behavior, conservation, and adaptive evolution. Future studies of the gut microbiome of NHPs will offer new insight into primate ecology and evolution as well as human health. They will also provide a new theoretical basis and means for primate conservation.