The levels of fasting-state serum bile acids (BAs) in individuals with polycystic ovary syndrome (PCOS) differ from those of control subjects. However, there is a lack of research on the BAs profile in lean women with PCOS and whether these changes are linked to the host metabolism. Therefore, our objective was to investigate the synthesis and metabolism of serum BAs in lean women with PCOS and assess the correlation between BAs and clinical characteristics. This study employed a cross-sectional design of lean women with PCOS (n = 240) in comparison to a control group (n = 80) consisting of healthy lean women. The findings revealed significant increases in the levels of non-12-OH BAs and chenodeoxycholic acid (CDCA)% (both P < 0.05) in lean women with PCOS. Additionally, a positive correlation was observed between CDCA% and total testosterone (T) (r = 0.130, P = 0.044) and free androgen index (FAI) (r = 0.153, P = 0.019). Furthermore, a decreased ratio of cholic acid/chenodeoxycholic acid (CA/CDCA) (P < 0.001) was observed in lean women with PCOS, suggesting the depletion or downregulation of CYP8B1. Receiver operating characteristic curve analysis indicated that the combination of CDCA/CA and DHEAS could potentially be used as a characteristic factor for PCOS in lean women. It is possible that enzymatic modifications in the liver could play a role in regulating hyperandrogenism in this specific subgroup of lean women with PCOS.