Polycystic ovary syndrome (PCOS) is a complex endocrine disorder in women of reproductive age. It is characterized by hyperandrogenism, menstrual disorders, and polycystic ovarian morphology. Insulin resistance (IR) is commonly associated with PCOS, and patients are at heightened risk for developing metabolic and endocrine comorbidities such as type 2 diabetes mellitus, cardiovascular disease, and endometrial cancer. Globally, PCOS has intensified rapidly, making it a major public health issue with a significant economic burden on the healthcare system. The heterogeneous nature of the syndrome has produced considerable scientific debate, and the current treatment strategies are often unsatisfactory. The application of omics research in PCOS has contributed to a greater understanding and identification of novel biomarkers and targets. To provide a focused, mechanistic, and in-depth discussion, this chapter focuses specifically on the genetic expression and epigenetic mechanisms implicated in PCOS progression and advancement. Special insight has been given into how plant-derived compounds may modulate these molecular pathways to offer innovative therapeutic interventions.