Background Complementary remedies such as the Chinese herb ‘Sheng Ma’ (Black cohosh; Actaea racemose ‘AR’) are being sought to surmount the shortcomings of conventional hormonal and surgical therapies developed in the treatment of polycystic ovary syndrome (PCOS). However, the AR hepatotoxicity urges a cautionary warning to be labelled on its products as recommended by the United States Pharmacopeia where 4 out of 7 hepatotoxic cases in Sweden were possibly associated with black cohosh products.Methods We investigated the efficacy, safety and molecular targets of black cohosh ethanolic extract and/or vitamin C on ovarian functionality, oxidative response in the hyperandrogenism-induced PCOS alongside with holistic profiling of its arsenal of secondary metabolites using UPLC-Qtof-MS. A well-established rat model using oral letrozole, daily, for 21 days was employed then the rats received the AR extract with and without vitamin C for 28 days. The hormonal evaluation, antioxidant status, histopathological examination, immunohistochemical analysis, cell proliferation, apoptosis, and the expression ratio of the aromatase (Cyp19α1) gene were evaluated.Results Beneficial effects were exerted by AR in PCOS rats via the improved antioxidant status, hormonal profile, lipid profile, glucose level, liver functions, curtailed percentage of apoptotic cells and the induced Ki-67 expression in the granulosa, theca cell layers and interstitial stromal cells. Notably, AR combination with vitamin C was not only more effective to reverse the dysregulated levels of testosterone, luteinising hormone, and mRNA level of Cyp19α1 gene in the PCOS rat, but also safer, while the combination regulated both ovarian and hepatic MDA and GSH levels with a histologic improvement noticed in livers and ovaries. In addition, the untargeted metabolomic profiling enabled the identification of 61 metabolites allocated in five major chemical classes.Conclusion This study demonstrated the benefit of the combination between AR and vitamin C in mitigating the reproductive and metabolic disorders of PCOS with the elimination of AR hepatotoxic risk.