Taking the party performance and value identity as indexes of the teaching effect of ideology and political theory course, we researched on the teaching effect of ideology and political theory course in universities and colleges by using structural equation modeling (SEM) based on our investigation in universities and colleges of Chongqing. The results show that: 1) University students hold low performance identity and middle value identity of the governing party; 2) The ideology and political theory course can influence university students from two paths which are the direct path (the theory course→value identity) and the indirect path (the theory course→performance identity→value identity). The indirect path is more important and its effect is contributed mainly by the mediation variable performance identity; and 3) The teaching attitude have the most important impacts on value identity compared to teaching contents and teaching styles.