The ban on bisphenol A (BPA) has led to a rapid increase in the use of BPA analogs, and they are increasingly being detected in the natural environment and biological organisms. Studies have pointed out that BPA analogs can lead to adverse health outcomes. However, their interference with ovarian tissue has not been fully elucidated. In this study, seven- to eight-week-old CD-1 mice were exposed to corn oil containing 300 μg/kg/day bisphenol B (BPB) or bisphenol AF (BPAF) through oral gavage, and ovarian tissues were collected at 14 and 28 days of exposure. Ovarian toxicity was evaluated by the ovarian index, ovarian area, and follicle number. mRNA-seq was used to identify differentially expressed genes (DEGs) and infer the association of DEGs with ovarian diseases. BPB or BPAF exposure induced morphological changes in ovarian tissue in CD-1 mice. In addition, Gene Ontology (GO) analysis revealed disturbances in biological processes (BP) associated with steroid biosynthetic process (GO:0006694) and cellular calcium ion homeostasis (GO:0006874). Subsequently, regulatory networks of BPA analogs (BPB or BPAF)-DEGs-ovarian diseases were constructed. Importantly, the expression levels of DEGs and transcription factors (TFs) associated with ovarian disease were altered. BPB or BPAF exposure causes damage to ovarian morphology through the synergistic effects of multiple biological processes and may be associated with altered mRNA expression profiles as a risk factor for ovarian diseases.