Background <p>Women with polycystic ovary syndrome (PCOS) have a high incidence of pregnancy and obstetric complications. Anti-Müllerian hormone (AMH) is closely related to reproductive outcomes. The potential relationship between AMH levels and the occurrence of late miscarriage in these patients remains unclear.</p> Methods <p>This study enrolled 1,831 patients diagnosed with PCOS who achieved clinical pregnancy following their first frozen-thawed embryo transfer cycles. The patients were categorized into miscarriage group and live birth group according to their pregnancy outcomes. The relationship between AMH levels and the occurrence of late miscarriage in this population was assessed before and after propensity score matching.</p> Results <p>PCOS patients with late miscarriage exhibited elevated AMH levels compared with those who had a live birth. According to univariate logistic regression analysis, each 1 ng/mL elevation in AMH level was related to a 6.3% increased risk of late miscarriage (odds ratio [OR], 1.063; 95% CI, 1.027–1.101; <i>P</i> = 0.001). After adjustment for confounding factors, the risk of late miscarriage increased by 5.6% (adjusted OR = 1.056, 95% CI: 1.012–1.101, adjusted <i>P</i> = 0.011). The odds of late miscarriage increased by 63.5% in the 50th percentile group (OR, 1.635; 95%CI, 1.129–2.369; <i>P</i> = 0.009), by 68.0% in the 75th percentile group (OR, 1.680; 95%CI, 1.141–2.474; <i>P</i> = 0.009) and by 93.8% in the 90th percentile group (OR, 1.938; 95%CI, 1.164–3.228; <i>P</i> = 0.011) when compared to the live birth group. After PSM, circulating AMH levels remained strongly linked to the occurrence of late miscarriage. The AUC of AMH for predicting late miscarriage was 0.614 (95% CI, 0.564–0.664; <i>P</i> = 0.000), with an optimal cutoff value of 10.395 ng/mL.</p> Conclusions <p>High pre-pregnancy circulating AMH levels (especially &gt; 10.395ng/mL) is associated with a high risk of late miscarriage in patients with PCOS undergoing FET.</p> Trial registration <p>N/A.</p>