Background Polycystic ovarian syndrome (PCOS) is a prevalent endocrine disorder among reproductive age women, characterized by an array of metabolic and reproductive dysfunctions, including hyperandrogenism, ovarian cysts, and insulin resistance. Obesity, an aggravating factor in PCOS, intensifies its metabolic and histological manifestations, complicating disease management. This study explores how obesity influences early histological, biochemical, and radiological features in women with PCOS, with a comparative analysis between obese and non-obese groups. Method This cross-sectional comparative study was carried out over the period from ‘January 2023 to January 2024’ City Hospital, Peshawar. A purposive sample of 101 women aged 18–35 diagnosed with PCOS according to Rotterdam criteria was categorized into obese and non obese groups based on BMI (≥30 kg/m² for obese). Data collection involved three stages: histological (ovarian stroma, cysts, inflammation, fibrosis), biochemical (hormonal and metabolic profiles), and radiological (ultrasound imaging of ovaries and endometrial thickness). SPSS 26 ‘was used for data analysis, with p-values <0.05 indicating statistical significance’. Results Conclusion Keywords Obese women showed significantly greater ovarian stroma thickness (p=0.001), more frequent follicular cysts (p=0.003), higher inflammation rates (p=0.015), and fibrosis presence (p=0.023) than non-obese women. Biochemical analysis revealed elevated luteinizing hormone (p=0.004), testosterone (p=0.002), and insulin levels (p=0.001) among obese participants. Metabolic indicators, including fasting glucose, cholesterol, triglycerides, and HOMA-IR, were higher in obese women, indicating greater metabolic dysfunction (p<0.05). Radiological features showed higher antral follicle counts (p=0.002), ovarian volume (p=0.017), and endometrial thickness (p=0.003) in obese participants. Obesity exacerbates histological, biochemical, and radiological features in women with PCOS, suggesting a need for weight and metabolic management strategies to reduce symptom severity and prevent long-term complications. These findings highlight the role of individualized care in managing PCOS, with targeted interventions for obese patients.