Objective To compare changes in microbial diversity in the intestines of male and female rats with obesity and depression. Methods An obesity and depression model was established by feeding rats a high fat diet and the cums classic depression making method. SD rats were randomly divided into control group (Group C), obese group (Group F), the depression group (Group Y), the obesity and depression group (Group FY). Five months were required for modeling. Depression-like behavior was evaluated by the sugared water preference test, open field test, and forced swimming test. The serum estrogen level and blood lipids were measured. Fecal samples were also collected. Highthroughput sequencing of 16S rDNA was performed and the result were analyzed by bioinformation analysis software. Changes in intestinal flora diversity of rats in each group were compared. Results Obesity depression model rats were successfully established by a high-fat diet and cums method in the same countries. The estrogen level of obesity and obesity depression female rats was significantly increased, while there no significant difference was observed in the estrogen level between male groups. There was a significant difference in diversity of intestinal flora in Group FY. The B/ F value was lower than that of in obesity and depression groups, and the B/ F value of obesity and depression in male rats was only approximately half that of female rats. At the genus level, changes in Blautia and the other eight flora in the Group FY and Group F of male and female rats were consistent, but changes in a small number of flora in Bacteroides and other genera in females and males were inconsistent. In the male and female obesity and depression model, there were differences in the composition of Gram-positive and -negative bacteria among the intestinal flora. The composition of G⁺ was Firmicutes and actinomycetes, but the proportions were different. G^- males mainly had Firmicutes, Bacteroides, and desulfitobacteria, whereas females mainly had Bacteroides, verruciformis, and desulfitobacteria with different composition ratios. Conclusions Significant changes in the composition and structure of intestinal flora in male and female obese and depressed rats may be related to estrogen.