Background: In China, large-scale population movement and increased childcare costs have brought about a "care crisis" for rural children left-behind when their parents migrate to cities. The unprecedented scale of internal population migration poses multiple challenges to the health of left-behind children in rural areas. Rural left-behind children are currently experiencing insufficient caregiving capacity of intergenerational guardians; the impact of serious parental absences; inadequate nutritional and dietary support and healthy behaviours; limited health service utilization; and abnormally high levels of poor mental health.Purpose: Using 2016 China Family Panel Studies’ micro-data two issues were explored: What is the current status of health inequality in rural left-behind children, including the degree of health inequality and differences in health inequalities of left-behind children in different regions and different age groups; and, second, what are the socioeconomic factors (income deprivation, access to medical services, migrating parents) and inter-generational care arrangements that impacted the health inequality of left-behind children? Method: The health indicators of left-behind children were measured by the concentration index (CI), and the contribution of each socio-economic variable to health inequality was decomposed through the RIF-I-OLS model.Results: The health inequality of left-behind children in rural areas was pro-rich. Left-behind children under 5 years of age had the highest health inequality in all regions; the availability of medical services had a significant negative impact on the health inequality of left-behind children in rural areas, especially in the western provinces; income deprivation had a significant positive effect on the health inequality of left-behind children in rural areas, most notably in the eastern provinces; migrant parents had a negative, and intergenerational caregivers a positive, impact on the health inequality of left-behind children; and left-behind children in the western provinces suffered the largest negative impact on their health. Finally, left-behind children experienced relative health inequality due to their sex, education level and health endowments. Policy recommendations are advanced to address issues of health inequalities in rural left-behind children.