<p>Studies have reported the beneficial effect of family functioning on the healthy development of adolescents. However, the full picture of the relationship between family functioning and problem behaviors in left-behind adolescents (LBA) remains unclear. The current study utilized a cross-sectional design to explore the relationship between family functioning and problem behaviors in 4716 Chinese LBA, who were come from Henan, Shandong and Sichuan Provinces of China. Analysis of covariance was applied to test the difference between LBA and non-LBA in family functioning, positive cognition, social support and problem behaviors, and structural equation modeling was used to test the relationship of them in LBA. The results showed that problem behaviors of LBA were more severe than non-LBA. Family functioning had a negative effect on problem behaviors in LBA, and family functioning affected problem behaviors directly and indirectly through positive cognition among LBA. Moreover, the indirect effect of family functioning on problem behaviors of LBA via positive cognition was moderated by social support. Social support strengthened the indirect effect, while the conditional indirect effect was greater when social support was high than when it was low. The findings of current study highlight the importance of enhancing positive cognition and social support to maximize the positive effect of family functioning on preventing problem behavior among LBA.</p>