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There is an association between physical and mental health, but little is known about the pathways from one to the other under the influence of family functioning among adolescents. In this study, we conducted bidirectional mediation analysis to explore how mental health (physical health) mediated the relationship between family functioning and physical health (mental health). We found that adolescents with better physical status were more likely to have better mental health, and vice versa. Family functioning could directly influence each of them or indirectly influence it through the other. Our results suggested that we may not only intervene in mental health to improve physical health for adolescents, but also, we could improve their mental health by changing their physical status.