This paper constructs a structural equation model of the implementation mechanism of the Civics and Politics teaching in compulsory physical education courses, taking teaching methods and teaching organization as mediating indicators to test the mediating effect. Combined with the existing results of the construction of the physical education curriculum Civics, it designs and constructs the integrated construction model of physical education curriculum Civics for the whole academic period and optimizes the structure of digital effectiveness of the construction of the physical education curriculum Civics, by designing and conducting comparative experiments to explore the teaching effect of the implementation of the flipped classroom teaching mode in the Civics and Politics of Physical Education in colleges and universities. Analyze the methods and means of teaching Civics and evaluate them for the construction of college sports courses in the context of deep learning. Conduct empirical research on the integration of Civic politics elements in sports courses, analyzing the degree of students’ cognition and mastery of Civic politics elements and the application and change of students’ Civic politics elements. The analysis shows that the confidence interval of teaching content→teaching methods→teaching organization→Civics and politics goal achievement is 0.005-0.048, the effect value is 0.018, and the p-value is 0.008. It proves that the teaching methods and teaching organization play a chain mediating effect in the influence of teaching content on the achievement of Civics and politics goals.