The deep integration of ideological and political education in courses with professional education is a core measure to implement the fundamental task of fostering virtue and nurturing talent and to promote the connotative development of higher education. Based on the logic of the Ministry of Education’s “four high integrations”, the integration mechanism is manifested as the dialectical unity of knowledge imparting and value guidance, the symbiotic synergy of explicit education and implicit education, the mutual support of practical exploration and theoretical research, and the organic combination of coordinated advancement and classified measures. The current integration practice faces predicaments such as cognitive bias, superficial element mining, stiff instructional design, and the absence of an evaluation system. It is necessary to promote the integration of the two from “formal integration” to “connotative integration” through four paths: conceptual innovation, content reconstruction, method innovation, and mechanism guarantee, to achieve the trinity of value shaping, knowledge imparting, and ability cultivation.