With the rapid development of China’s economy, a large number of farmers have gone to cities to work in order to improve their family’s economic conditions. Their children were forced to be separated from their parents and stay in the countryside to become left-behind children. Due to lack of parental upbringing, they fail to form a high-level parent-child attachment. Therefore, compared with non-left-behind children, left-behind children were more likely to have problem behaviors. According to the Social Psychological Model of Problem Behavior, the study of problem behaviors should consider both external environmental factors and individual internal factors. In addition to co-parenting and parent-child attachment, the factors of left-behind children themselves are also closely related to their problem behaviors. Therefore, based on the Social Psychological Model of Problem Behavior, our study aimed to explore the influence of paternal co-parenting on the problem behaviors of left-behind children and the mediating effect of paternal attachment and self-esteem. A total of 613 left-behind children were investigated from Anhui province. With the consent of the school, parents, and students, the students completed the Paternal Co-parenting Questionnaire, Father-child Attachment Questionnaire, Self-Esteem Scale, and Strengths and Difficulties Questionnaire. The average age of these left-behind children was 9.63 ± 0.92, there were 400 male students, 213 female students, 308 belonging to the “father-absent” group, accounting for 50.20%, and 250 belonging to the “parents absent” group, accounting for 40.80%. The data were analyzed using correlation analysis, structural equation modeling by SPSS25.0 and Mplus 8.3. Correlation analysis showed that positive paternal co-parenting was positively related with paternal attachment and self-esteem, but not significantly correlated with problem behaviors; negative paternal co-parenting was negatively correlated with self-esteem, positively correlated with problem behaviors, paternal attachment, and self-esteem, but not significantly correlated with paternal attachment. The results of the structural equation model showed that the positive co-parenting of fathers significantly negatively predicted the problem behaviors of left-behind children, while the negative co-parenting of fathers significantly positively predicted the problem behaviors of left-behind children. Father-child attachment played an insignificant role in the mediation between the co-parenting of fathers and the problem behaviors of left-behind children, while self-esteem played a significant role in the mediation between the co-parenting of fathers and the problem behaviors of left-behind children. Father-child attachment and self-esteem played a chain role in the mediation between the co-parenting of fathers and the problem behaviors of left-behind children. This result shows that even in left-behind families where fathers are mainly absent, the role of fathers is still irreplaceable. At the same time, it also suggests that we should not only pay more attention to the problem behaviors of left-behind children but also focus on the positive quality of left-behind children themselves. Reducing the problem behaviors of left-behind children does not mean promoting their positive development. Therefore, it is equally important to improve the self-esteem of left-behind children. It also supports the left-behind children in a new perspective of both “reducing problems” and “promoting development”, so that left-behind children can develop actively even in an unfavorable environment.