Changes in the composition and ratio of the flora during colitis have been found to potentially affect ovarian function through nutrient absorption. However, the mechanisms have not been fully explored. To investigate whether colitis-induced dysbacteriosis of the intestinal flora affects ovarian function, mice were given dextran sodium sulfate (DSS) through drinking water. High-throughput sequencing technology was used to clarify the composition and proportion of bacterial flora as well as gene expression changes in the colon. Changes in follicle type, number, and hormone secretion in the ovary were detected. The results showed that 2.5% DSS could induce severe colitis symptoms, including increased inflammatory cell infiltration, severe damage to the crypt, and high expression of inflammatory factors. Moreover, vitamin A synthesis metabolism-related genesRdh10,Aldh1a1,Cyp26a1,Cyp26b1, andRarβwere significantly decreased, as well as the levels of the steroid hormone synthase-related proteins STAR and CYP11A1. The levels of estradiol, progesterone, and Anti-Mullerian hormone as well as the quality of oocytes decreased significantly. The significantly changed abundances ofAlistipes,Helicobacter,Bacteroides, and some other flora had potentially important roles. DSS-induced colitis and impaired vitamin A absorption reduced ovarian function.