The Research of program design course class teaching based on self-organization theory.The paper introduced the concept of self-organization theory and designed the class teaching of program design from the viewpoint of the self-organization. It is tyring to solve the student’s passive learning and other problems that happened in the program design course class teaching. It is also trying to build the student-centered class teaching system and improve the quality of personel training to the high level. It analyzed the program design class teaching self-organization characteristics and teaching practice. Finally it provided some methods to build the self-organization, including opening teaching system and promoting students to do more collaborative interaction and paying attention to teaching feedback.