Objective: To explore the relationship between fruit intake and the risk of overweight with obesity in children, so as to provide references for the prevention of childhood obesity. Methods: From September to November 2014, a stratified cluster sampling method was used to select 6 369 children aged 6-12 from two elementary schools of a country in rural Chongqing for physical examinations and questionnaire surveys, and 1 814 children in grades 1-2 at baseline were followed up from March to May 2019. The relationship between fruit intake and the prevalence of overweight and obesity was analyzed. Results: According to the percentile of fruit intake, the 6 369 children at baseline were assigned to three groups: Q 1 (< P 33.3 , fruit intake <100 g/d), Q 2 ( P 33.3 - P 66.7 , fruit intake:100-214.3 g/d), and Q 3 (> P 66.7 , fruit intake >214.3 g/d). For the baseline survey results, children in the Q 2 group had a lower weight and Body Mass Index (BMI) ( P <0.05); the prevalence of overweight and obesity among children in the Q 1 group was the highest (32.03%), and the prevalence of overweight and obesity among boys in the Q 2 group was the lowest (31.94%) after gender stratification ( P <0.05). The follow up survey results showed no significant differences between the three groups in terms of changes in height, weight, and BMI ( P >0.05); but the prevalence of obesity among youth in the Q 2 group was the lowest (5.07%, P <0.05). Compared with youth in the Q 2 group, the risk of obesity was higher among those in the Q 1 group at baseline survey ( OR=1.41, 95%CI=1.10-1.81, P <0.05), and was higher among those in the Q 3 group at follow up survey ( RR= 1.83, 95%CI=1.21-2.75, P <0.05). Conclusion Deviating from moderate fruit intake may increase the likelihood of overweight and obesity in children, and it is recommended that children are encouraged to consume fruits as part of a well balanced diet to prevent the occurrence of obesity.