With the development of science and technology, brain science has obtained fruitful results, which have been widely applied in many fields. For physical education (PE), it is also of great significance to apply the results of brain science research. In order to optimize physical education and teaching methods, this paper explores the possibility of combining brain science with physical education, and studies the application of brain science in physical education and teaching. It then proposes PE teaching arrangements and methods according to the latest brain science research results such as the whole brain theory and the imagery thinking theory. The research results of this paper provide the basis for scientifically formulating the content and objectives of the PE curriculum, and also can promote the scientific and standardized development of physical education and teaching.