The problems of left-behind children in China have attracted widespread attention from researchers. However, previous empirical studies on left-behind children have mostly been based on small samples and small-scale surveys and have not covered all age groups. Whether left-behind children fare worse than their non-left-behind counterparts remains unknown. We conducted the first nationwide survey to examine whether left-behind children aged 0-6 years old have poorer interactions with primary caregivers and whether left-behind school-age children experience higher levels of victimization and emotional distress than their non-left-behind counterparts. A total of 25,297 children or primary caregivers from 27 counties in 12 provinces of China participated in our survey. The results indicated that left-behind children aged 3-6 years old had poorer interactions with primary caregivers and that left-behind school-age children experienced higher levels of victimization and emotional distress than their non-left-behind counterparts. Multiple linear regression analyses further found that being left behind was a significant predictor of interaction status, victimization and emotional distress. The present study provides important perspectives for improving the well-being of left-behind children, particularly regarding the need to focus on the quality of care, victimization and emotional distress of left-behind children.