Abstract: Major water conservancy projects have a high degree of complexity and great social influence,and their top-level governance structure design imposes a profound impact on project transaction governance and project management performance. Since the reform and opening-up in China, the structure has been evolving accordingly with the changes in the socioeconomic system. This paper conducts a long period, large span analysis of multiple cases on typical major water conservancy projects,and finds out that since the reform and opening-up, the top-level governance structure of the projects has evolved through three stages: the stage of the government’s role as the project owner, the stage of the project legal persons’ responsibility system led by the government, and the stage for promotion of a better combination of efficient markets and competent governments. We also find that the governance framework "government-led + market mechanism" is suitable for the situation of the socialist market economy with Chinese characteristics. Generally, project entity formation modes should be analyzed with consideration of the investment and financing mode; the optimal design of top-level governance structure should be formulated in combination with project characteristics. This study enriches the top-level theory in the theoretical governance framework of major engineering projects, useful for their top-level governance structure design.