In polycystic ovary syndrome (PCOS), ectopic fat accumulation remains debatable. Therefore, intra-abdominal, hepatic, and epicardial fat were compared between PCOS women and body mass index (BMI)-matched controls and their associations with metabolic and hormonal parameters were explored. Furthermore, the performance of echocardiographic epicardial adipose tissue thickness (EATT) and hepatic steatosis measurement using transient elastography-based controlled attenuation parameter (TE-CAP) in screening abdominal visceral adipose tissue (VAT) was originally evaluated. Women aged 18-39 years with BMI < 35 kg/m² were recruited. PCOS was defined by the Rotterdam criteria. All participants underwent clinical and laboratory exams, dual-energy X-ray absorptiometry (DXA), TE-CAP, and echocardiography. A receiver operating characteristic curve was applied to evaluate the accuracy and optimal cutoff values of TE-CAP and EATT in predicting DXA-measured VAT. The study included 35 women with PCOS and 37 controls. PCOS women exhibited higher levels of androgens, insulin resistance (IR) parameters, LDL-cholesterol, triglycerides, VAT, and EATT. VAT correlated with IR and triglycerides, whereas EATT correlated with HDL-cholesterol. In PCOS women aged 18-29, the cutoff values of CAP and EATT for VAT were 198.0 and 3.07, respectively, with CAP showing higher area under the curves (AUC). In PCOS women aged 30-39, the cutoff values were 209.5 and 3.36, respectively, with EATT showing higher AUC. VAT correlates with more metabolic parameters in PCOS than TE-CAP or EATT. TE-CAP is useful for VAT screening in PCOS patients aged 18-39 years, whereas EATT is effective and outperforms CAP in those aged 30-39 years.