Polycystic ovary syndrome (PCOS) is a complex heterogeneous endocrine disease affected by genetic and environmental factors. In this manuscript, we aimed to describe the composition of bile acid metabolomics in the follicular fluid (FF) of PCOS. The FF was collected from 31 control patients and 35 PCOS patients diagnosed according to the Rotterdam diagnostic criteria. The Bile Acid Assay Kit and ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) were used in this study to detect the total bile acid and 24 bile acid metabolites. Glycocholic acid (GC3A), taurocholic acid (TCA), glycochenodeoxycholic acid (GCDCA), and chenodeoxycholic acid-3-β-d-glucuronide (CDCA-3Gln) were elevated in the PCOS group. GCDCA was positively correlated with the serum follicle-stimulating hormone (FSH) (r = 0.3787, p = 0.0017) and luteinizing hormone (LH) (r = 0.2670, p = 0.0302). The level of CDCA-3Gln also rose with the increase in antral follicle counts (AFC) (r = 0.3247, p = 0.0078). Compared with the control group, the primary bile acids (p = 0.0207) and conjugated bile acids (p = 0.0283) were elevated in PCOS. For the first time, our study described the changes in bile acid metabolomics in the FF of PCOS patients, suggesting that bile acids may play an important role in the pathogenesis of PCOS.