Background Advancements in ultrasound technology have facilitated identifying polycystic ovarian morphology (PCOM) in women with and without polycystic ovary syndrome (PCOS), but it still has limitations due to follicle counting methods and variation of phenotypes according to ethnicity. Ethnicity-specific ovarian morphology may help to establish ethnicity-specific follicle count cut points for defining PCOM in women with PCOS. Objectives To investigate the prevalence and factors associated with PCOM in Thai women of a reproductive age with PCOS. Methods This prospective cross-sectional study was conducted in our gynecology department at a tertiary teaching hospital from February 2016 to May 2017. We included women with PCOS, who were measured for weight, height, waist circumference, and blood pressure. Blood samples were taken to measure fasting blood glucose, lipid profile, testosterone level, and 2 h post-load 75 g oral glucose tolerance test (OGTT). Transvaginal or transrectal sonography was performed to evaluate their ovaries. Results All 143 patient participants we included had oligomenorrhea, 77.6% of them had acne, and 64.3% hirsutism. Their average total testosterone level was 0.47 ± 0.10 ng/mL. The prevalence of PCOM was 55.2%. The proportions of PCOM diagnosed by ovarian follicle and ovarian volume criteria were 36.4% and 42.0%, respectively. There were 20.0 ± 9.5 follicles per ovary, 8.3 ± 3.1 follicles per cross section, and the mean ovarian volume was 7.9 ± 3.0 mL. Conclusion The overall prevalence of PCOM in Thai women of reproductive age with PCOS was 55.2%. Our univariate analysis found no factors significantly associated with PCOM.