Abstract: Aligning disciplinary and program offerings with national strategic needs is a key issue in building China into a leading country in education. With its cross-border institutional environment and reform-oriented experimental functions, the Guangdong-Hong Kong-Macao Greater Bay Area offers a distinctive site for examining cooperative higher education in China. Taking four representative cooperative higher education institutions in the Greater Bay Area as cases, this study analyzes the evolution of their program offerings. The findings show that the program configuration of these institutions has shifted from a "foundational expansion" aimed at building comprehensive universities in the early stage to a "mission-oriented configuration" that is closely connected with national strategies and directed toward frontier fields and interdisciplinary fields. In terms of level structure, the recent "graduate-first, undergraduate-later" pathway does not simply reflect an emphasis on high-level talent training; it also represents an institutional adaptation and strategic choice through which institutions balance compliance and feasibility under multiple institutional constraints. These structural changes are jointly driven by the transition of macro-level policy from general regulation to strategic guidance, the continuing strategic interaction among multiple governance actors at the meso level, and the micro-level use of a dual-track degree system involving domestic and overseas degree arrangements to reconcile compliance with innovation. On this basis, future development should focus on refining the regulatory space for program approval and adjustment, improving institutional rules, and strengthening collaborative mechanisms. It is also necessary to build a dynamic program-adjustment mechanism linked to talent-demand forecasting and early warning, thereby developing a practice model with both regional characteristics and wider applicability. Such efforts will promote the transformation of program offerings in cooperative universities from static planning to dynamic regulation and provide replicable experience for higher education in serving national strategic needs.