Abstract: The Guangdong-Macao In-Depth Cooperation Zone in Hengqin is a new practice of cross-border governance under the "one country, two systems" principle. Comparatively speaking, it has the rigid constraints of "two systems", which determines that foreign theories and experiences are difficult to be used. However, the three typical cross-border cooperation zones of Haut-Rhin, Oresund and Berlin-Brandenburg still have important implications for the construction of cross regional collaborative governance systems for the Guangdong-Macao In-Depth Cooperation Zone in Hengqin. Based on the Institutional Analysis and Development Framework (IAD) theory, this paper summarizes the commonalities of cross-border governance between the three typical international cross-border cooperation zones and Guangdong-Macao In-Depth Cooperation Zone in Hengqin, and conducts a horizontal comparative analysis of their differences. It is found that there is reference value for the Guangdong-Macao In-Depth Cooperation Zone in Hengqin in terms of organizational coordination, institutional coordination, and interest coordination, namely, establish and improve legal coordination mechanisms; Clarify the power and responsibility relationship of governance subjects, fully absorb social forces to participate widely; Strengthen resource integration and promote the integration and convergence of social and livelihood; Build an institutionalized communication and coordination mechanism guided by industrial cooperation; Accelerate the implementation of the policy of establishing a normalized evaluation mechanism for the cooperation zone, and promote the scientific and rational decision-making process for the cooperation zone.