Abstract: Education of moral and core values (EMCV) in colleges and universities faces a structural coupling dilemma in the digital era. This dilemma arises from the heterogeneity among intelligent interaction subjects, paired with the homogenization in value guidance. The logic of multi-agent empowerment in the digital transformation of EMCV in higher education institutions is reflected in four key aspects. Firstly, multi-agent collaboration helps achieve dual gain effects in individual and group interactions. Secondly, the fusion of group personalization drives innovative learning approaches during digital transformation. Thirdly, intelligent resource distribution ensures educational equity through data-driven resource allocation. Fourthly, adaptive educational models are supported by intelligent systems and dynamic feedback-driven optimization. However, practical challenges arise from the integration of intelligent systems on multi-agent platforms, as well as the profound contradiction between digital objectives and content adaptation. Moreover, ethical risks concerning data privacy in intelligent teaching also pose significant issues. Additionally, there is the issue of the role reshaping of both teachers and students in terms of digital adaptability. Therefore, China should develop a comprehensive technological framework to advance its EMCV in fours aspects. (1) This framework should focus on platform construction, content innovation, equity assurance, and the transformation of teachers’ role. (2) This involves designing and implementing a multi-agent collaborative platform that defines the operational model for integrating resources and efforts across different stakeholders. (3) This initiative aims to comprehensively upgrade the content of ideological and political courses to foster learning innovation. It has the parallel goal of reinforcing principles of fair and transparent data management to optimize educational equity mechanisms. (4) A key aspect is the deep transformation of teachers’ roles, shifting their competencies from being primary knowledge transmitters to becoming facilitators of students’learning.