Abstract: In recent years, many colleges and universities have made a lot of explorations and attempts in the process of ideological and political course reform and innovation, but problems such as formalization, entertainment, fragmentation, knowledge and utilitarianism still stand out. These problems are fundamentally caused by the separation of political nature and academic rationality in ideological and political courses. In this regard, Xi Jinping proposed that the reform and innovation of ideological and political course should "adhere to the unity of political nature and academic rationality". In order to achieve the unity of political and academic rationality of ideological and political courses in colleges and universities, we must first establish the guidance of "guiding theory by politics and promoting politics by theory", and form a coordination mechanism including "establishing a benign teacher-student interaction mechanism" and "optimizing and upgrading the assessment and evaluation model".