Assessing the mental health problems encountered by school children and understanding the contributing factors are crucial to inform strategies aimed at improving mental health in low-resource contexts. However, few studies have investigated the mental health problems among disadvantaged children in poorer countries. This study examines the prevalence of mental health problems in rural China and their association with child and family characteristics. The study uses survey data from 9696 children in 120 rural primary schools and measures child mental health using the Strengths and Difficulties Questionnaire (SDQ). Overall, 17.9% of the sample children were found to be in the abnormal range of the SDQ total difficulties scores. The mean score was 12.93 (SD = 4.94). Abnormal scores were associated with child and family characteristics, including older child age (Odds Ratio, OR = 0.704, 95% CI: 0.611, 0.810; p < 0.001), gender (OR = 1.235, 95% CI: 1.112, 1.371; p < 0.001), and academic performance (OR = 0.421, 95% CI: 0.369, 0.480; p < 0.001). Reading time was found to be protective for mental health. Risk factors include excessive screen time (OR = 1.685, 95% CI: 1.409, 2.016; p < 0.001) and being bullied (OR = 3.695, 95% CI: 3.301, 4.136; p < 0.001). Our study suggests that future mental health illness prevention programs in rural China should consider targeting different aspects of children’s social contexts.