This paper attempts to establish a new educational methodology for the theoretical system of basketball education in order to further investigate the ideological basis, basic principles, and value and significance of basketball education. The study achieves this purpose by integrating cognitive science and educational psychology into the PEDAGOGY model. Firstly, it organizes the basic philosophy of basketball education, then integrates cognitive science and educational psychology into the PEDAGOGY model, reforms and innovates the current basketball education, and designs the basketball teaching mode after the model is innovated. Finally, in order to investigate whether the basketball teaching quality is affected after the innovation of the PEDAGOGY model, the main factors affecting the basketball teaching quality are screened by the factor analysis model and the EM algorithm. Through the empirical analysis, the basketball course teaching factor has the largest contribution rate of 25.632%, in which the loadings of embodied cognition reached 0.865 and psychological counseling reached 0.875, indicating that the PEDAGOGY model integrating cognitive science and educational psychology is the main factor affecting the quality of basketball teaching.