Abstract: Innovating the governance system in the Greater Bay Area with institutional mechanisms as the core is of great theoretical and practical significance for the governance efficiency of the construction of a world-class urban agglomeration in the Greater Bay Area. Under the background of"one country, two systems", the Guangdong-Hong Kong-Macao Greater Bay Area is a cross-border and cross-institutional urban agglomeration. It is necessary to examine and plan its governance system innovation by drawing on international experience and taking into account China's national conditions and the special situation of Guangdong-Hong Kong-Macao regional governance. According to the three-dimensional integrated analysis framework of "value, structure and function" of China's national governance system in the new era, the governance system of world-class urban agglomeration in the Guangdong-Hong Kong-Macao Greater Bay Area should choose the path of a three-horizontal four-vertical framework. First, the four values of stability, efficiency, openness and sharing should be upheld to guide the practice of innovating the governance system of the Greater Bay Area urban agglomeration. Second, the integrated national governance system, the administrative coordination governance mechanism, the market integration governance model and the social integration governance policy should be innovated through the reform of the governance structure. Third, the functional adjustments, including stable and orderly politics, efficient and coordinated administration, open and developed market, and coordinated and shared society, should be achieved so as to build a community of shared future for the Guangdong-Hong Kong-Macao Greater Bay Area urban agglomeration.