Propofol is widely used to induce and maintain anesthesia during gynecological surgery and assisted reproduction. However, few studies have investigated the influence of propofol on ovarian function and the related mechanism. In this study, propofol was administered to female mice, and ovarian function was evaluated by measuring serum AMH levels, follicle counts, and expression of related proteins. IOSE-80 and KGN cells were treated with propofol to assess mitochondrial function and mitophagy using fluorescence staining, ROS and mitochondrial membrane potential assays, and Western blotting. Recombinant TGF-β1 was applied both in vivo and in vitro to investigate the involvement of the TGF-β/SMAD2/3 signaling pathway. These results showed that propofol reduced the serum AMH level and the number of follicles in the mice ovaries, downregulated the protein expressions of FSHR and CYP19A1, and facilitated ovarian cell apoptosis both in vivo and in vitro. Treatment with propofol significantly decreased the mitochondrial fluorescence intensity and increased mitophagy fluorescence in IOSE-80 and KGN cells. Additionally, propofol enhanced ROS generation, decreased mitochondrial membrane potential and increased the levels of proteins associated with mitophagy (LC3B, PINK1, PARKIN). Propofol lessened the abundance of TGF-β1, SMAD2/3 and phosphorylated-SMAD2/3. Co-treatment with recombinant TGF-β1 significantly increased cell survival, reduced apoptosis, and upregulated the protein expression levels of FSHR, CYP19A1, PINK1, and PARKIN in IOSE-80 and KGN cells. These results demonstrated that propofol over-activates mitophagy through the TGF-β/SMAD2/3 pathway, and thus affects ovarian function. This finding provides some guidance for women with fertility needs when choosing anesthesia drugs for surgery.