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Background Dental caries have a serious impact on general health and well-being; however, there is a lack of relevant data on the development trends of dental caries in permanent teeth among 12-year-old children in China. We aim to assess long-term trends of dental caries in permanent teeth among 12-year-old children in China and identify the susceptible subgroups based on five consecutive national surveys from 1995 to 2014. Methods A total of 88 972 subjects were extracted from five consecutive national surveys (1995, 2000, 2005, 2010, 2014). Standardized dental examinations were conducted and the oral health status of each subject was recorded. The prevalence of Decayed, Missing and Filled teeth (DMF%), mean Decayed, Missing, Filled teeth score (DMFT) and Caries Filling Ratio (CFR) were used as measurement indicators. Cochran–Armitage trend test was used to evaluate the trends in DMF% and CFR, and multivariate linear regression was used to evaluate the trends in DMFT. Results A V-shaped fluctuating upward trend in DMF% during 1995–2014 was observed (Z = − 13.124, P β = 0.057, P P > 0.05), and the CFR in 1995–2014 was 17.4%, 22.8%, 19.3%, 23.4% and 15.6%. The DMF% and DMFT of rural children had a larger absolute increase than that of urban children during 1995–2014 (DMF%-urban: Z = − 0.242, P > 0.05; DMF%-rural: Z = − 19.036, P β = 0.035, P β = 0.077, P (P (P Conclusions Over the past 20 years, DMFT and DMF% of 12-year-old children in China presented V-shaped fluctuant upward trends, with a decline trend from 1995 to 2000 and an upward trend from 2000 to 2014. CFR had no significant improvement. The rural children and girls are the more vulnerable groups in the development of dental caries and need to pay priority. Our study supports the continuation of policies to improve children’ oral health.