Objective: To understand mental health status of primary school boarding pupils in rural families, and to explore specific intervention method suitable for mental health problems prevention and intervention among those children. Methods: Social emotional education was administered through family station among 105 rural primary school students in Gaohawo central primary school in Yanchi county of Ningxia Province. Mental health was evaluated by the Mental Health Rate Scale for Pupil (MHRSP) before and after intervention. Results: The average score of mental health of children with rural boarding students was (48.00±18.56), the detection rate of total score ≥65 was 19.05%, and the detection rate of with at least one dimension≥10 points was 100%. Mental health problems in different dimension was highest in personality defects (48.57%), followed by learning disabilities (43.81%), emotional disorders (25.71%), social adjustment disorders (18.10%) and morality defects (11.43%). After the intervention, the detection rate and total score of mental health problems among rural pupils decreased significantly compared to before intervention (χ2=20.60, 6.05, 43.58, 10.99, 12.73, P<0.05), and the detection rate of learning disabilities, mood disorders, personality disorders, social adaptation disorders, and moral defects decreased significantly (t=4.00, 3.31, 3.25, 3.31, 2.54, P<0.05). Conclusion Mental health problems of primary school students in rural areas are outstanding. Social and emotional education should be the focus of parents, schools, the community, as well as government. The social and emotional education of the "family station" activity could improve mental health among primary school pupils in rural areas, which is worth further promotion.