The construction of the Guangdong-Hong Kong-Macao Greater Bay Area, as a significant regional development strategy of the nation, poses an urgent demand for cross-border cooperation in higher education. In recent years, the Greater Bay Area has achieved breakthroughs in the field of Sino-foreign and Mainland-Hong Kong-Macao cooperative education, forming a new pattern of two-way mobility. However, the institutional complexity of “one country, two systems, three legal jurisdictions, and three customs territories” presents unique “Bay Area Paradoxes” for cooperative education in terms of legal applicability, governance structure, resource allocation, and cultural identity. Based on empirical investigations into the current state of higher education integration in the Greater Bay Area, this paper delves into the underlying institutional barriers faced by cross-border education and proposes systematic breakthrough pathways from three dimensions: legal construction, governance transformation, and connotative development, aiming to provide theoretical references for constructing an internationally competitive higher education cluster in the Bay Area.