Intestinal microorganisms that living in the mucosa and contents of the gastrointestinal tract of animals, have close links with their hosts over a long evolutionary history. The community structure of the fish intestinal microbiota is associated with food, living environment, and the growth stage. To screen for potential probiotics that can be used for regulating breeding behaviors, this study focused on the diversity of fish intestinal microorganisms. This study aimed to investigate the effects of sex and body weight on the intestinal microbial diversity ofGymnocypris chilianensisin the wild. The results showed that the significant high diversity and richness of intestinal microbiota were fould in heavier individuals, and males. The dominant bacterial phyla ofG. chilianensiswere Proteobacteria, Firmicutes, and Bacteroidetes. In addition, the abundance of Firmicutes varied significantly among different body weights. The genus profile revealed that small individuals were dominated byWeissella, while females were dominated byAeromonas, and both large individuals and males were dominated by other genera. Phylogenetic relationships and UPGMA clustering analysis showed significant differences among the groups. In general, the two main factors that have an effect on the intestinal microbiota diversity of wildG. chilianensisare sex and body weight.