To understand the incidence of school violence and its related factors among senior students in rural primary schools in Guizhou and Anhui provinces in 2016. From September to November 2016, one county was randomly selected from 47 impoverished counties of Guizhou and one county was randomly selected from 18 impoverished counties of Anhui Province by using multi-stage cluster sampling method. A total of 4 schools were randomly selected from primary schools which had more than 70% students with rural resident registration in each selected county, and 3 classes were randomly selected from fifth and sixth grades of each selected school. All students in each selected class were included in this study. A total of 2 521 students were included, and 2 506 valid questionnaires were collected with an effective response rate about 99.4%. Self-designed questionnaires were used to collect data on individual information, family information, and the incidence of school violence with related factors. Multivariable logistic regression was conducted to analyze related factors of school violence. The incidence of violence in rural primary schools was 50.4% (1 264/2 506) in 2016. The number of students who had physical assault, fought or been bullied was 682 (27.2%), 689 (27.5%) and 764 (30.5%), respectively. The results of multivariable logistic regression showed that the (95) values of incidence of school violence for male students was 2.13(1.78-2.54) compared with female students; and the (95) values of incidence of school violence for students with high peer acceptance, high family intimacy, more physical activity and mother who had education background of junior high school, senior high school, technical secondary school and junior college, bachelor's degree or above were 0.39 (0.26-0.57), 0.47 (0.40-0.57), 0.64 (0.52-0.78), 0.79 (0.66-0.96), and 0.65 (0.46-0.92) compared with those with low peer acceptance, low family intimacy, less physical activity and mother who had primary education and below. The incidence of violence in rural primary schools is not optimistic. Gender, peer acceptance, family intimacy, physical activity and mother education are related to school violence.