In the context of science professionalism, a social contractual relationship characterized by principal-agent form has been generated between politics and science. And in this relationship, truth seeking and efficiency of science are the basic requirements. Because of the information asymmetry between politics and science, the adverse selection of political subjects and the moral hazard of research are caused, damaging the truth seeking and efficiency of science. Therefore, it is inevitable that audit and supervision of research should become a necessary way to maintain a reasonable social contractual relationship. However, there are some difficulties in the practice of audit and supervision. In order to dispel these difficulties,we have to go deep into the various social relationships where“exchange” can take place based on the analytical methods of contractual relationship. By doing so, we can re-recognize the science-society contract. Thus, we can become clear of the main stakeholders of contractual relationship. Analysis based on the theory of organic boundary in this thesis believes that research audit agency should be a platform on which stakeholders of contractual relationship can cooperate with each other to investigate the truth seeking and efficiency of science research. Meanwhile, the thesis also believes that audit and supervision of science research should be an organic boundary activity between science and politics.