Abstract Gut flora undergoes a dynamic colonization and development process at different stages of human life. Sex specific gut flora development begins during puberty, which is influenced by sex hormone levels. The potential relationship between sex hormone levels, which suggests that there may be a two way interaction between intestinal flora and sex hormones. In addition, evidence is emerging for bidirectional effects of the microbiome in human health. Therefore, the review presents the dimorphism of intestinal flora, the characteristics of intestinal flora during puberty and the latest research progress, explores the close relationship between intestinal flora and precocious puberty and reproductive system diseases, and further explains the influence mechanism and treatment measures of considering gender factors in intestinal microflora, precocious puberty and reproductive system related diseases.