Background/AimCangfu Daotan Wan (CFDTW) has been widely used for polycystic ovary syndrome (PCOS) patients in the type of stagnation of phlegm and dampness. In this study, we aimed to evaluate the mechanism underlying the therapeutic effect of CFDTW on PCOS with phlegm-dampness syndrome (PDS).MethodsIn silicoanalysis was adopted to identify CFDTW potential targets and the downstream pathways in the treatment of PCOS. Expression of PKP3 was examined in the ovarian granulosa cells from PCOS patients with PDS and rat PCOS models induced by dehydroepiandrosterone (DHEA). PKP3/ERCC1 was overexpressed or underexpressed or combined with CFDTW treatment in ovarian granulosa cells to assay the effect of CFDTW on ovarian granulosa cell functionsviathe PKP3/MAPK/ERCC1 axis.ResultsClinical samples and ovarian granulosa cells of rat models were characterized by hypomethylated PKP3 promoter and upregulated PKP3 expression. CFDTW reduced PKP3 expression by enhancing the methylation of PKP3 promoter, leading to proliferation of ovarian granulosa cells, increasing S and G2/M phase-arrested cells, and arresting their apoptosis. PKP3 augmented ERCC1 expression by activating the MAPK pathway. In addition, CFDTW facilitated the proliferation of ovarian granulosa cells and repressed their apoptosis by regulating PKP3/MAPK/ERCC1 axis.ConclusionTaken together, this study illuminates how CFDTW confers therapeutic effects on PCOS patients with PDS, which may offer a novel theranostic marker in PCOS.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13048-023-01200-7.