The purpose of this study is to clarify the relationship between self-determination motivation and peer relationship and physical education class alienation in middle school students. The results of this study can be used as basic data for physical education teachers who want to minimize alienation of physical education class. In this study, 200 middle school students from three middle schools in Jeonju city and 195 middle school students from three middle schools in JiLin city were selected as sample subjects using the convenience sampling method. The approach I adopt to solve the problem is analyzed by t-test, one-way ANOVA, multiple regression analysis, correlation analysis and stepwise regression analysis using SPSS 23.0 version. As a result of the t-test according to gender, autonomy, competence, and motivation were higher in boys than girls. On the other hand, the factor of physical education facilities alienation, athletic clothing alienation, and class contents alienation was higher in girls than boys. The results obtained in this research include according to the comparison between genders within the country, in Korea boys are more than girls. Concerned about self- determination motivation and peer relationship, Chinese girls showed differences in attention. In addition, Korean female students have shown great concern in the physical education class alienation. It can be seen from the research and analysis of the relationship between Self-determination motivation, peer relationship, and physical education class alienation of Korean and Chinese middle school students and various factors that the data differences in the correlation analysis are unbalanced.As a result of the regression analysis, first, the peer relationships were found to have a positive effect on the physical education class alienation. Second, positive emotions among the sub-factors of Intrinsic-Identified motivation and companion continuity were found to have negative effects on physical education class alienation in Korea. On the contrary, all China middle schools are positively affected.The considering the different effects of self-determination motivation and peer relationship to each type of physical education class, it is necessary to seek and apply measures to minimize the physical education class alienation. If so, it is considered that the alienation phenomenon of physical education class can be minimized and prevented in advance.