This study aimed to determine how pathological Internet use and emotional intelligence affect the relationship between perceived personal discrimination and problem behavior of left behind children. Data were collected from 406 left-behind students from 6 rural primary and secondary schools in Mainland China. Results indicated that perceived personal discrimination could be a predictor of left-behind children’s pathological Internet use, and further cause their problem behavior. Pathological Internet use had a partial mediating effect on the relation between perceived personal discrimination and problem behavior. In addition, emotional intelligence played a moderating role in the relationship between perceived personal discrimination and problem behavior, as well as between pathological Internet use and problem behavior. Emotional intelligence could alleviate the negative impact of perceived personal discrimination on problem behavior, as well as the negative impact of pathological Internet use on problem behavior.