Behavioral strengths and difficulties among children and adolescents may be significantly associated with their academic performance; however, the evidence on this issue for rural youth in developing contexts is limited. This study explored the prevalence and correlates of mental health from three specific dimensions—internalizing problems, externalizing problems, and prosocial behavior—measured by the Strengths and Difficulties Questionnaire (SDQ), and the association of these dimensions with academic performance in math among a sample of 1500 students in rural China. Our findings indicated that students in rural China had worse behavioral difficulties and poorer prosocial skills when compared to most past studies conducted inside and outside of China. In addition, total difficulties and prosocial scores on the SDQ were significantly associated with student math test scores, as students whose externalizing, internalizing, and prosocial scores were in the abnormal range scored lower in math by 0.35 SD, 0.23 SD, and 0.33 SD, respectively. The results add to the growing body of empirical evidence related to the links between social environment, mental health, and academic performance in developing countries, highlighting the importance of students’ mental health for their academic performance, and of understanding risk factors in the social environment among rural youth in developing countries.