Abstract As evaluation has become the norm in Higher Education in Taiwan, we have witnessed how the evaluation has brought the positive self-perspective on organizations. After years of its implementations, however, there is the need to look back into the evaluation system, its concept and impacts it has brought to higher education from different angles of perspective, reflecting on the evaluation behaviors in the hope to emerge with better coping strategies. This article begins with a discussion on the background context and development of the evaluation system on higher education in Taiwan. It discusses the actual evaluation accreditation system and its impacts on government and society. It further questions the problems of university autonomy and accountability under this framework of evaluation. At the same time, it examines the relationship between the goals of evaluation and the world trend. The conclusion mainly uses initiative motivation, autonomous development and reflective feedback as the main structure of the discussions; and explains the mechanism in the operation and mechanism of higher education evaluation. When institutions take into account the regulations from education authorities, competition for resources and responses toward evaluation officer’s feedback and demand, the fulfillment of the main character of the institution is the major concern. In other words, taking into account the core values of evaluation and giving impetus to practices, the construction of the self-characteristics of the institution maybe more important.