Objective: To investigate the prevalence of emotional and behavioral problems and related factors of left-behind children in impoverished rural China (mainly in the first grade of junior high school). Methods: A cross-sectional survey of rural households in 27 poverty-stricken counties in 12 provinces across China was conducted using the Strengths and Difficulties Questionnaire (SDQ). Results: The prevalence of emotional and behavioral problems in left-behind children was 11.7%, and that of non-left-behind children was 8.9%. There was statistical difference between the two groups (P < 0.01). There are no differences between the two groups in terms of the various factors of SDQ. The incidence of insomnia in the left-behind group was 58.3%, which was higher than that in the non-left-behind group 50.9% (P < 0.01); loneliness (62.1% vs. 51.8%, P <0.01); running away from home (23.1% vs. 18.8%, P < 0.01), and self-injury behavior (16.8% vs. 12.2%, P < 0.01). Left-behind children are more likely to have negative psychological feelings including insomnia, loneliness, self-injury, and run away from home. They also experienced more bullying including maliciously teased by peers, intentionally excluded or isolated, physically threatened or intimidated. All of these factors are associated with their abnormal emotional and behavioural development. Conclusion: The incidence of emotional and behavioral problems of left-behind children in rural areas in poverty-stricken areas is significantly higher than that of non-left-behind children; Logistic regression analysis showed that bullying behavior and abnormal psychological characteristics are significantly associated with left-behind adolescents abnormal emotional and behavioral development.