In recent years, China’s education and teaching reform has become a hot issue. The emergence of flipped classroom teaching model has greatly changed the conventional teaching mode. This paper uses the methods of literature, questionnaire, teaching experiment, interview, classroom observation and mathematical statistics to study the effect of flipping classroom teaching mode in PE and Health Teaching in rural primary schools. The research shows that the flipped classroom teaching mode in PE and Health Teaching in rural primary schools is helpful for students to master movement technology and improve students’ attitude and interest in PE learning. In contrast, the emotional performance and cooperative spirit of the experimental class students who adopt the flipped classroom teaching mode are improved more significantly. Compared with the conventional classroom teaching method, the flipped classroom teaching mode has no obvious difference in the influence of students’ physical fitness test results. The research suggests that we should strengthen the skill training of PE teachers and constantly improve their teaching ability, constantly enrich teaching methods under the flipped classroom teaching mode. When implementing the flipped classroom teaching mode, we should design a more reasonable teaching scheme in combination with the characteristics of students in rural schools, encourage scholars to actively study the research of flipped classroom teaching mode, and promote the reform and development of PE and Health Teaching in rural primary schools.