With the acceleration of China’s industrialization and urbanization, there is a large number of left-behind children in China who are reported with more challenges in development. The study aims to analyze the differences in family socioeconomic status (SES) and discrimination perception between left-behind children and non-left-behind children and further explore whether SES or discrimination perception has a greater impact on the problem behaviors of left-behind children. We found the family SES of left-behind children was significantly lower than that of non-left-behind children; left-behind children’s perceived discrimination was significantly higher than that of non-left-behind children; perceived discrimination of left-behind children had a greater impact on their problem behavior than the family SES.