Abstract: As a national strategy for regional development, the construction of Guangdong-Hong Kong-Macao Greater Bay Area must rely on the power of education cooperation to undertake the missions of regional innovation, development and integration. The education systems in Guangdong, Hong Kong and Macao are very different, not only in terms of student source, but also in terms of industrial support and employment capacity, furthermore in the terms of their international academic reputation. According to the above realistic foundation, the practical principles of education cooperation in the Greater Bay Area can be further explored. Specifically, it is necessary to coordinate different choices such as short-term goals and long-term goals, and to consider both system construction and partial breakthroughs. It is also necessary to choose between one-way input and two-way complementation, single-power mode and multi-joint mode of education exchange and cooperation. Besides, it is important to find out the benchmark and reference object for the construction of the Greater Bay Area, and to insist on using interdisciplinary and cross-border research methods to explore the issues of education cooperation in this Greater Bay Area.