This paper aims to analyze the factors that influence the effects of MOOC-based teaching in universities and find an effective way to make the advantages of MOOCs be better played. Considering the factors affecting MOOC-based teaching are complicated, we take a university course (Ideological and Political Education) as an example to analyze the influence factors by using ISM and MICMAC model. Combining ISM and MICMAC models can further analyze the hierarchical structure and overall relationship of influence factors on the teaching effect of MOOCs. Based on existing researches, we firstly select 10 principal factors that affect the teaching effects of MOOC-based courses (IPE courses). Second, we set up an adjacency matrix to clarify the basic binary relations between these factors, find the reachability matrix by exponentiation, and obtain a 5-hierarchy Interpretive Structural Model. Third, based on the MICMAC analysis, we get a new idea for the optimization of MOOC-based teaching. Finally, through a detailed discussion of the results, we provide some suggestions to optimize the teaching effect of MOOCs in the IPE courses. This study is of great significance for optimizing MOOC-based teaching and provides workable methods and ideas for improving the teaching effect of MOOCs in university courses.