Purpose: Dental health is associated with the growth and development, physical or psychological, of children. Although numerous preventive measures are available, dental caries among primary schoolchildren remains a public health concern in China. Understanding the disparity of children's dental health between rural and urban areas in China could provide further insight into the prevention of caries. Methods: A cross-sectional study was conducted to examine the oral health of pupils aged 6-12 years in Pudong District (Shanghai) and Lichuan (Jiangxi Province) in China. A questionnaire survey was performed among children's guardians to identify the potential risk factors for childhood dental caries. Results: A total of 1922 primary schoolchildren were included in this study, with 815 from Pudong and 1107 from Lichuan. The mean age of children from Pudong was 8.57 (SD = 1.61), which was statistically significantly lower than their counterpart from Lichuan (9.36 ± 1.75). The prevalence of caries in Pudong and Lichuan was 63.4% and 75.0%, respectively. Statistically significant differences of demographical and behavioural features were observed between schoolchildren in Pudong and Lichuan. In general, Lichuan children had a higher caries risk compared with their Pudong counterparts (OR = 3.43, 95%CI 2.65-4.28). Moreover, the non-parental caregivers, low family income, low parental educational level, as well as bad dietary habits, were identified as risk factors for caries. Conclusions: Childhood caries in the rural area was far more severe than that in the urban area. This disparity was determined by several factors such as the high proportion of left-behind children in the rural area (e.g. children who remain in rural regions of China while their parents leave to work in urban areas). Our government should put the prevention of caries among rural children at a higher priority in the near future to narrow the gap between rural and urban areas. Keywords: children, China, dental caries, rural city, urban city