Abstract: Hengqin has entered a new era of joint construction, joint management and sharing. With the promulgation of the Overall Plan for the Construction of the Hengqin Guangdong-Macao Deep Cooperation Zone, the Hengqin Guangdong-Macao Deep Cooperation Zone has formed a new system of joint discussion, joint construction, joint management and sharing, leaving behind the loose cooperation in the form of joint meetings and moving towards institutionalized and standardized close cooperation.. The joint management system of Hengqin Guangdong-Macao Deep Cooperation Zone has formed a distinct institutional framework of "leadership, decision-making and executive levels", which contains the institutional characteristics of "multi-level government and common governance", and embodies the institutional innovation of "merging Macao Special Administrative Region into Hengqin management system", "mutually adjusted multi-level governance" and "integration of government and governance". The Hengqin co-management system is facing the challenges of cross-regional governance, cross-border governance and cross-system governance. In the future, the Hengqin Guangdong-Macao Deep Cooperation Zone should continue to innovate and improve the co-management system, improve the central government's overall coordination ability and the Guangdong-Macao government's cooperative governance ability.