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 fared 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 poor interactions with primary caregivers, and whether 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, for children aged 3–6 years old, left-behind children had poor interactions with primary caregivers than non-left-behind children; for school-age children, left-behind children experienced higher levels of victimization and emotional distress. Multiple linear regression analyses further found that being left-behind was a significant predictor of interaction status, victimization and emotional distress. The present study provided 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.