Projecting the burden of thyroid cancer (TC) over time provides essential information to effectively plan measures for its management and prevention. This research obtained data from the Global Burden of Disease (GBD) Study from between 1990 and 2019 to model how TC will affect China until 2039 by conducting the Bayesian age-period-cohort analysis. The number of new TC cases in China was 10,030 in 1990, 39,080 in 2019, and is projected to be 47,820 in 2039. This corresponds to 3,320, 7,240, and 4,160 deaths, respectively. Disability-adjusted life years (DALYs) cases increased from 103,490 in 1990 to 187,320 in 2019. The age-standardized rate (ASR) of incidence increased from 1.01 to 2.05 during 1990-2019 and was projected to increase to 3.37 per 100,000 person-years until 2039. The ASR of mortality (ASMR) remained stable during the study period and was projected to have a mild decline from 0.39 to 0.29/100,000 during 2020-2039. Although the ASMR in male patients has maintained increasing at a rate of 2.2% per year over the past 30 years, it is expected to decline at a rate of 1.07% per year in 2019-2039. The most significant increase in crude incidence occurred in people aged 45-65 from 1990 to 2019, however, this will shift into young people aged 10-24 from 2020 to 2039. In addition, the proportion of deaths and DALYs caused by obesity increased from 1990 to 2019 and affected men more than women. In conclusion, a substantial increase in counts of incidence of TC in China is projected over the next two decades, combined with the slightly declining mortality, indicating that rational health policies are needed in the future to cope with the increasing number of TC patients, especially among males and adolescents.