Analyzing principal-agent problem between executives and controlling shareholders has very important roles based on the characteristic of single controlling shareholder in Chinese listing company under the framework of principal agent theory. This paper introduces reputation incentive mechanism based on the assumption of both executives and controlling shareholders are bounded rational. Then it uses evolutionary game theory to analyze the process of motivate executives, the interactive mechanism of whether the executives work hard or not and whether controlling shareholders supervise or not. It reveals the evolutional process of executives and controlling shareholders in the principal-agent relationship based on the consideration of reputation. And then the paper analyzes the key factors which impact the stability of dynamic system. The results show that there doesn't exist optimal stability strategy but with three local stability strategies. Finally, it proposes to design reasonable incentive mechanism in order to make principal-agent mechanism converge to an ideal state of optimal aim, through combined explicit incentive mechanism such as stock rights and stock option, beef up the penalties for shirking and opportunistic behaviors of executives and implicit incentive mechanism such as hire high reputation executives to make managers' personal interest close to company interest.