Purpose <p>Polycystic ovary syndrome (PCOS) is a common endocrinological disorder closely associated with metabolic dysfunction. Metabolic dysfunction-associated steatotic liver disease (MASLD) is a new comprehensive term encompassing metabolic dysregulation and hepatic steatosis. This study aims to evaluate the diagnostic performance of the hepatic steatosis index (HSI), fatty liver index (FLI), and metabolic parameters in detecting MASLD among PCOS patients. It also aims to explore the prevalence of MASLD across PCOS phenotypes to assess phenotype-specific risks.</p> Methods <p>A retrospective analysis of 1,192 women aged 18–40 years with PCOS, diagnosed based on the Rotterdam criteria, was conducted. Participants were categorized into two groups: MASLD and non-MASLD. Clinical and metabolic parameters were analyzed, including body mass index (BMI), waist-to-hip ratio, lipid profiles, homeostatic model assessment for insulin resistance (HOMA-IR), and liver enzymes. HSI and FLI scores were calculated, and their diagnostic performance was assessed using ROC analysis. Subgroup analysis evaluated the prevalence of MASLD among PCOS phenotypes (A, B, C, D). Multivariate logistic regression identified independent predictors of MASLD.</p> Results <p>MASLD prevalence was 25.8%. HSI (AUC: 0.88) and FLI (AUC: 0.89) demonstrated strong diagnostic performance. MASLD patients had significantly higher BMI, HOMA-IR, and triglyceride levels, and lower high-density lipoprotein levels (<i>p</i> &lt; 0.001). Phenotypes A and B exhibited the highest risk of MASLD, with hyperandrogenism emerging as a key factor (<i>p</i> &lt; 0.004).</p> Conclusion <p>HSI, FLI, and metabolic parameters are practical, non-invasive tools for diagnosing MASLD in PCOS patients. Routine screening using these indices may help clinicians detect and manage MASLD early. To reduce MASLD risk, phenotype-specific treatments targeting obesity, insulin resistance, and hyperandrogenism may be recommended.</p>