The practice of Body Building plays a very important role in trainers’science movements. If they can do it according to Physiology and Sports training theory, they will get more from less. This paper made analysis of teaching methods in basketball fitness movements that adopted in college sports selective courses from the point of physiology theory, so as to provide data base to basketball fitness research and theoretical evidence to the selection of teaching methods through the teaching effects reflected by physiological index values. In this paper, firstly analyzed the characteristics of traditional teaching method and free selective course teaching method, then chose the reasonable experimental control way according the two teaching methods characteristics, made design of 8 weeks teaching experiments, finally achieved the advantages and disadvantages of the two teaching methods by before and after experiments physiology index data as well as inter-group data matched test value and differences significant correlations. It could be seen from research results that the second kind of practice obvious has an advantage over the first kind ones.