In recent years, research on the intestinal microbial communities and human health has developed rapidly. However, the regulation and application of the intestinal microbial community are still in their infancy. The reason for this is that our understanding of the structure and function of the human gut microbiome is inadequate. Synthetic microbiota is a new microbial community established by artificial synthesis of multiple species, which is simulated, tested, and optimized by various experimental models and mathematical modeling methods in vitro and in vivo. It is helpful to deepen the understanding of the structure, stability, and functional activity of the complex microbiota in the human gut. We summarized the research methods of the intestinal microbiome, the factors affecting the stability of the intestinal microbiome, and the challenges facing the synthesis of the intestinal microbiome, in order to provide a reference for the bidirectional transformation of the theoretical research and clinical application of intestinal microbial community.