The estimate of dental caries among Chinese children at the microscale level using standard methodology remains unclear. In this study, we assessed and analyzed the disease burden of childhood dental caries in China by extracting data from the Global Burden of Disease, Injuries, and Risk Factors Study 2016 (GBD 2016). In 2016, the number of cases, prevalence, years lived with disability (YLD), and age-standardized YLD rate of dental caries was 93.0 million, 43.0%, 32,200 person years, and 14.8 per 100,000, respectively. Across 33 provincial units, the disease burden was highest in Hubei (YLD rate 28.6 per 100,000), lowest in Macao (9.1 per 100,000), while geographical clustering was not observed. Compared with 1990, the prevalence in 2016 decreased from 46.8% to 43.0%, and the YLD rate decreased from 16.5 per 100,000 to 14.8 per 100,000. Given the slight decrease in dental caries burden, the prevalence and disease burden remained high among Chinese children. Strategies for addressing the spatial inequity of childhood dental caries require geographical targeting.