The top-level governance of megaprojects refers to the governance level of government side and project entity, which affects all kinds of transaction governance. In order to solve the problem that the behavior of the project entity changes with the situation, and the top-level governance mechanism of the project using agency theory or steward theory alone can neither adapt to the complex and changeable environment, nor adapt to the characteristics of the complex person of the project entity, a solution combining the two theories is proposed. Two questions are answered at the theoretical level. First, the project entity is complex person between the agent and the steward. Second, integrating agency theory and stewardship theory with trust as the bond, so as to optimize the current top-level governance mechanism of projects dominated by agency theory. The top-level projects governance mechanism after integration of the two theories includes communication, risk sharing, spiritual incentive, authorization, material incentive and control supervision under the guidance of agency theory and stewardship theory, and plays a role of guiding the stewardship behavior and restraining its opportunistic behavior from different angles of the project entity.