Objective To investigate the prevalence and related factors of emotional and behavioral problems in rural left-behind children aged 3 to 5 years. Methods A cross-sectional survey was conducted to investigate the prevalence of emotional and behavioral abnormalities among 5 050 children aged 3 to 5 years in 27 poverty-stricken counties of 12 provinces across China using the Strengths and Difficulties Questionnaire （SDQ）. Results The prevalence of emotional and behavioral problems in left-behind children was 13.3% （140/ 1 046）， and that of non-left-behind children was 14.7% （590/4 005）. There was no statistical difference between the two groups （χ2 =1.237，P=0.266）. The prevalence of peer association abnormalities in the left-behind children group was 5.0% （52/1 046） lower than that in the non-left-behind group （7.2%，287/4 005）， and there was a statistical difference （χ2 =6.732，P=0.012）. Logistic regression analysis showed that the primary caregivers agreed that corporal punishment increased the risk of emotional and behavioral problems in left-behind children （OR=1.655， 95%CI=1.121-2.444）. Conclusions There is no difference in the prevalence of behavioral problems between left-behind children and non-left-behind children aged 3 to 5 years. Supporting corporal punishment increases the risk of emotional and behavioral problems in left-behind children.