Owing to its capacity to damage the endocrine system, bisphenol A (BPA) is being substituted in common consumer products by chemically related compounds, including bisphenol F (BPF) and bisphenol S (BPS). Although BPF and BPS in body fluids are comparable in concentration and frequency to BPA, the toxicity of these analogs in female reproduction remains largely unknown. Using a nontargeted metabolomics technique, this study aimed to examine the effect of BPF and BPS exposure on the metabolism of human ovarian granulosa (KGN) cells. Analysis of the differentially expressed metabolites (DEMs) identified 991 and 609 DEMs in the KGN cells exposed to BPF and BPS, respectively, at three various concentrations (0.1, 1, and 10 µM), with BPF having a greater interfering effect than BPS. Specifically, exposure to low concentrations (0.1 µM) of both bisphenols more greatly affected cellular metabolism than exposure to higher concentrations. Metabolic pathway enrichment analysis using the KEGG database revealed that the mechanisms by which BPF and BPS induced toxicity in the granulosa cells were different: BPF exposure significantly altered purine metabolism, autophagy-related pathways, and ferroptosis, whereas BPS mainly interfered with one-carbon metabolism (vitamin B6, riboflavin, and folate). These results demonstrated the differences in the mechanisms by which BPF and BPS induced to granulosa cell dysfunction.