This paper researches on the impact on innovation by trust relationship in corporate governance mechanism and explores the complex behaviors emerging from the nonlinear interactions among board, CEO and R & D center, used agent-based modeling and simulation methods. The results show that agency theory and stewardship theory derived from trust have a significant impact on innovation. Agency theory emphasizes the control based on distrust, causing manager’s myopia behavior thus focusing on incremental innovation. Stewardship theory emphasizes the collaboration based on trust, managers often think from a strategic perspective and focus on radical innovation. The effective design of both control and collaboration in the corporate governance mechanism can promote the company’s innovation better.