Objective: To analyze the trends in the disease burden of polycystic ovary syndrome (PCOS) in China from 1990 to 2021, to evaluate the age-period-cohort effects, and to predict its prevalence trend from 2022 to 2035, thereby providing a reference for formulating targeted prevention and control strategies. Methods: Data on the incidence, prevalence, and disability adjusted life year (DALY) rate of PCOS in China were extracted from the 2021 study of Global Burden of Disease (GBD). Joinpoint regression analysis was used to assess temporal trends. The age-period-cohort model was employed to evaluate the effects of age, period, and birth cohort on the disease burden. The autoregressive integrated moving average (ARIMA) model was applied to predict the disease burden indicators from 2022 to 2035. Results: In 2021, the incident cases of PCOS in China were 130.4 thousand. The age-standardized incidence rate (ASIR) was 57.31 per 100 000, representing a 63.51% increase from 1990 (35.05 per 100 000). The number of prevalent cases was 9.481 5 million, with an age-standardized prevalence rate (ASPR) of 2 962.19 per 100 000, marking an 84.63% increase from 1990 (1 604.41 per 100 000). The DALY was 81.3 thousand person-years, and the age-standardized DALY rate (ASDR) was 25.57 per 100 000, showing a 86.23% increase from 1990 (13.73 per 100 000). Joinpoint regression indicated significant upward trends in ASIR, ASPR, and ASDR from 1990 to 2021, with average annual percent change (AAPC) of 1.61%, 2.02%, and 2.05%, respectively (all P<0.001). Age distribution showed that the peak age of incidence was 15-19 years. The prevalence peaked in the 25-29 years group, followed by the 30-34 years group. The DALY rate reached its peak at 20-24 years and remained at a high level at 25-39 years. Age-period-cohort model analysis showed that the DALY rate increased continuously with age. The period DALY rate ratio exhibited an upward trend over time; using the 2006 group as reference, the rate ratio of the 1991 group was 0.69, rising to 1.15 for the 2021 group. Compared with the 1975 birth cohort, the disease risk increased progressively for cohorts born in 1980 and later, with the DALY rate ratio peaking at 3.36 for the 2005 birth cohort. The ARIMA model demonstrated satisfactory goodness-of-fit (all R2≥0.999 8). It is predicted that by 2035, the ASIR, ASPR, and ASDR will reach 63.31 per 100 000, 3 615.43 per 100 000 and 31.16 per 100 000, corresponding to increases of 10.47%, 22.05% and 21.86% compared to 2021, respectively. Conclusions: The disease burden of PCOS in China increased continuously from 1990 to 2021, with the incidence peak concentrated in adolescents (15-19 years) and the increasing risk of birth cohort. Predictions indicate a continued significant rise in all disease burden indicators by 2035. Enhanced early prevention, control, and long-term management for women of reproductive age, particularly younger populations, are warranted.