The human gut microbiome, an essential component of the human digestive tract, is influenced by various elements including geographical location, ethnic background, dietary patterns, and genetic makeup. Geographical location, in particular, plays a significant role, as different regions in China exhibit distinct and unique bacterial groups. Furthermore, the impact of ethnicity on the composition of the gut microbiota should not be overlooked. In China, with its 56 ethnic subgroups, there exists an ethnic-specific clustering of gut microbiota, which contributes to a diverse range of microbial resources due to the presence of numerous minority groups. The relationship between gut microbiota and various diseases is an increasingly investigated area. Ethnic-specific gut microbiota can result in differences in disease incidence, and individuals from different ethnic groups may display variations in their gut microbiota when experiencing the same disease. The objective of this study is to present a comprehensive overview of the distinctive gut microbiome profiles across various regions and ethnic groups within China. This research highlights the unique characteristics of the gut microbiome among these minority populations and investigates the correlations between specific gut microbes and associated health conditions, a subject that remains underexplored in the current literature. This information will provide a basis for personalized medicine and the development of disease diagnostic models utilizing gut microbiota as biomarkers, thereby enabling more effective treatment plans and health management strategies.