Abstract Objectives: To investigate pregnancy outcomes after frozen-thawed embryo transfer (FET) according to polycystic ovary syndrome (PCOS) phenotypes. Design: Retrospective study. Setting: University-based centre for reproductive medicine. Participants: 8903 patients who underwent FET between January 2017 and October 2019. Methods: All patients were divided into PCOS and control groups, with the former categorised into four phenotype groups (PCOS phenotypes A, B, C, D) based on Rotterdam criteria. All patient data were retrospectively collected and evaluated. Main outcome measures: Pregnancy outcomes after FET consisted of biochemical, clinical and ectopic pregnancies, abortion, premature delivery and live birth. Results: Women with PCOS phenotype A experienced an increased incidence of biochemical pregnancy, clinical pregnancy and premature delivery compared to those with PCOS phenotype D and in the control group (P < 0.001, P = 0.005, P = 0.006, respectively), while incidences of ectopic pregnancy and live birth were comparable between all groups (P > 0.05). We found significantly higher abortion (P = 0.010) and lower ongoing pregnancy (P = 0.023) rates for women with PCOS phenotypes A and D compared to those in the control group. After adjusting for potential confounders, PCOS phenotypes A and D (vs. control) were associated with an elevated risk of abortion (adjusted odds ratio [OR], 1.476, 95% confidence interval [CI], 1.077–2.024, P = 0.016; adjusted OR, 1.348, 95% CI, 1.080–1.682, P = 0.008, respectively). Conclusions: For the first time, our study demonstrates that women with PCOS phenotypes A and D show an increased risk of abortion after FET.