This study analyzes the design and operation of multi-level governance system for the smooth delivery of infrastructure mega-projects with high institutional complexity caused by market transition. From an institutional perspective, this study scrutinizes the structure, elements, and dynamics of the governance system of infrastructure mega-projects and then proposes an integrative framework based on the inductive case study of the Hong Kong-Zhuhai-Macao Bridge mega-project. Multiple evidences of archives, field studies, and interviews related to the case project are triangulated to further analyze the institutional effects, specifically those with government logics and market structures, on the design and operation of the three-level governance system. Results reveal that the co-evolution between governments and markets in China has shaped the vertical levels of the mega-project governance system and has further affected their evolution and operation across various stages of project development. This study contributes to the rapidly emerging research on complex system governance by proposing a systematic model of three-level mega-project governance to enhance the timely delivery of infrastructure mega-projects within budget.