Background: Behavioral and emotional problems are common and often co-occur during childhood and adolescence. The aim of this study was to assess gender differences in the network structures of behavioral and emotional problems of children and adolescents in China based on a national survey. Methods: The Parent version of Achenbach' s Child Behavior Checklist (CBCL) was used to assess behavioral and emotional problems. To account for potential confounding factors in comparisons between boys and girls, propensity score matching was utilized. Network model differences were assessed using Network Comparison Test (NCT). Results: Data from 60,715 children and adolescents were included for analyses. Boys exhibited more severe total behavioral and emotional problems compared to girls. While several edges showed significant differences between boys and girls, the strongest association was consistently found between “Attention problems” (CBCL6) and “Aggressive behavior”(CBCL8) in both boys and girls, regardless of age. Network centrality was higher among adolescents compared to children. The most central problems commonly found across different genders and age groups were “Aggressive behavior” (CBCL8) (centrality values were 1.142 for boys aged 6–11 years, 1.051 for boys aged 12–16 years, 1.148 for girls aged 6–11 years, and 1.028 for girls aged 12–16 years), “Anxious/depressed” (CBCL1) (centrality values of 0.892 for boys aged between 6 and 11 years, 1.031 for boys aged 12–16 years, 0.951 for girls aged 6–11 years, and 1.099 for girls aged 12–16 years) and “Social problems” (CBCL4) (centrality values of 1.080 for boys aged 6–11 years, 0.978 for boys aged 12–16 years, 1.086 for girls aged between 6 and 11 years, and 0.929 for girls aged 12–16 years). Conclusion: Testing effective interventions that address aggressive behavior, anxiety/depression, and social problems may be beneficial for reducing risk of psychopathology among children and adolescents.