Objective To explore the prevalence and related factors of behavior problems among the high-grade primary school students (in Grade 4 to Grade 6) in Chongqing urban area. Methods By means of cross-sectional survey, a total of 3 137 high-grade primary school students in Chongqing urban area were investigated with Child Behavior Checklist (CBCL, version for parents) and self-designed basic information questionnaire. Results The relevance ratio of behavior problems was 27.26%. The univariate analysis revealed that type of school, grade, residential and family environment, and parental attitude toward children had effects on children’s behavior problems with significance difference (Plt;0.05). The stepwise regression revealed that grade, educational level of father, healthy conditions of parents, family structure, academic performance and parental attitude toward children were the independent and main influencing factors (Plt;0.05). Conclusion The relevance ratio of behavior problems among high-grade primary school students in Chongqing urban area is much higher, which is related to the following factors: family situation, parental attitude toward children, social and school environment. It indicates that the status of children’s mental heath is not optimistic in Chongqing urban area. Comprehensive measures combining family, school with psychologist should be taken to reduce the prevalence of behavioral problems.