Objective To explore the effect of Jiangzhipailuan decoction in regulating PPARα( belong to the nuclear receptor family of ligand-activated transcription factors ), PGC- 1α ( peroxime proliferator activated releptour)and SREBP-1c( belong to the baichelix-loop-helix-leucine zipper class of transcription factors), SCAP( SREBP cleavage activating protein) related to lipid metabolism in the treatment of polycystic ovarian syndrome. Methods 84 patients suffered polycystic ovary syndrome were randomly divided into 4 groups: one received traditional Chinese medicine treatment, one western medicine treatment, one combination therapy and one as the control group. Traditional Chinese medicine group was treated with Jiangzhipailuan decoction treatment for 3 months, western medicine group was treated with up to Diane-35 ( ethinyl cyproterone tablets) for three cycles, while the combination therapy group was treated with traditional Chinese medicine ,western medicine as well as combined treatment for 3 courses. Results In the combination therapy group the PPARα, PGC-1α and decreased SREBP-1c, SCAP copy number was significantly improved ,and body mass index was significantly lowered. The total improvement rate of menstrual in three groups were 71.42% ,75.00% ,92.86% respectively. Conclusion Jiangzhipailuan decoction played a prominent role in regulating PPARα,PGC-1α and SREBP-1c,SCAP related to lipid metabolism in the treatment of polycystic ovarian syndrome.