Follicular fluid is the microenvironment of oocytes that plays a crucial role in oocyte development. This study intended to explore the follicular fluid metabolomics in diminished ovarian reserve (DOR), polycystic ovarian syndrome (PCOS), and normal ovary response (NOR) groups. For metabolomic analysis, we collected the follicular fluid samples from 28 patients with DOR, 28 patients with NOR, and 28 patients with PCOS. The identified metabolites were annotated using KEGG to determine the metabolic pathway disturbances in PCOS and DOR. Based on the regression model, we conducted ROC analysis to identify PCOS and DOR biomarkers in the follicular fluid. The present results identified that the DOR and NOR groups' differential metabolites were primarily enriched in the choline pathway. The concentrations of pregnanediol-3-glucuronide and 2-hydroxyestrone sulfate in the DOR and NOR groups were substantially different. The metabolites in the purine metabolism pathway were mainly enriched in the PCOS and NOR groups. N-Acetyl-S-(N-methylcarbamoyl) cysteine and 3,4-dehydrothiomorpholine in the PCOS and NOR groups were substantially different. We also identified metabolic alterations in PCOS and DOR follicular fluid, which provides novel ways for PCOS and DOR diagnosis and therapy.