Internal migration in China has resulted in large numbers of left-behind children. Despite growing attention paid to this population, existing research has not systematically addressed the mediating mechanisms linking parental migration to children's health. The present study examines the influences of migration on the health of left-behind children in China and the mediating channels, using data from a new nationally representative survey. We compare three groups of rural children aged 3–15 years (N = 2473): those who were left behind by both parents, those who were left behind by one parent and those living with both non-migrant parents. Results show that the health of rural children left behind by both parents (but not by one parent) is worse than the health of children living with both parents. The health disadvantage of these children is mediated by their caregivers' poor health status and caregiving practices. These mediating factors not only have a direct impact on child health but also exert an indirect impact by shaping children's nutritional intakes. Contrary to conventional wisdom, monetary remittances are not a significant mechanism linking migration to child health.