Recently, performance auditing system of governmen is carried out as most promising framework of government audit. Performance audit by the Board of Audit and Inspection of Korea involves assessing the causes and effects of government policies, programs, and Institutions with the criteria of economy, efficiency, effectiveness. Performance auditing will contribute to strengthening the values of objective assessments of whether public resources are responsibly and effectively managed to achieve intended results. Nevertheless, there seems to be a problems appears in implementation of audit. That is the problems of tendency return to legitimacy audit which is result from the lack of strong approach and methodology. So, this study purpose to developing stronger audit concepts and methods that add to the process and framework of traditional performance auditing system. First, this study evaluates the limitation of current performance auditing system with the perspective of systems thinking. Second, this study analyzes the process and method of current system and develop the conceptual model of the Dynamics Audit System using the system dynamics methodology, which focused on the appropriate auditing process and framework.