The purpose of this paper is to analyze and research the practical activities of ideological and political education in colleges and universities using causal thinking design. Firstly, it studies the meaning and characteristics of ideological and political education and proposes a causal hypothesis. Secondly, the structural causal model is used to complete the basic structure of the causal thinking model, and the structural causal model is optimized using the HSIC Lasso method. Then, based on the Bayesian generative causal directional algorithm, the functional causal model is constructed, and the model is optimized. Based on the model, the Interaction Network Method for Civic Education Practice in Colleges and Universities is framed. Finally, based on the SCM algorithm, the learning effect of Civics in colleges and universities is analyzed. The Y → X and X → Y causal inference accuracy of the SCM algorithm is 100% and 90%, respectively. More than 70% of the students think that causal thinking exercises help to improve the learning effect of the Civics course.