Unintentional injury is the leading cause of childhood death and disability in many countries worldwide. This study aimed to quantify rates and risk factors for childhood unintentional injury in areas of rural China, where many children are left behind by migrant worker parents. We administered a questionnaire to children aged 9 to 15, in 56 schools in five counties in Zhejiang and Guizhou provinces. Of the 3791 respondents, 44% lived with both parents, 23% with one parent, and 33% with neither. Around half the children (47.9%) had suffered at least one unintentional injury in the past year, with burns (26%), animal bites (20%) and mechanical injury (18%) the most common. Left-behind children had no increased risk of unintentional injury, but children living in poorer Guizhou ( p = 0.001), of divorced parents ( p = 0.02), and less well-educated mothers ( p = 0.02) were associated with higher risk. Virtual absence of personal level risk factors highlights the importance of addressing environmental risk to reduce childhood injury. The findings have informed a community-based intervention to reduce injury risk through raising awareness of environmental hazards, and through removal of specific hazards. Importantly, the Chinese government should ensure that known effective interventions are subject to legislation and enforcement.