Higher education in Taiwan is facing competition and challenges from the macro environment of globalization. Taiwan’s key policy direction is enhancing university quality in order to respond to these future trends. Universities’ international competitiveness relies on not only faculty members’ teaching quality, but also their research performance. Faculty members’ research performance strongly affects a university’s reputation, funding generation, and attraction of international and local students. Reviewing the higher education development in Taiwan, although policymakers have continued to promote the benefits of differentiating universities, few studies care how environmental factors of different types of universities affect faculty members’ research performance. Currently, fewer studies focus on the influence of environmental factors on professors’ research performance. In addition, few studies have explored the structural inequalities between universities. This research contains two sequential research methods—namely, analytic hierarchy process and questionnaire survey—to accomplish the following purposes: exploring related literature; determining key indicators of environmental factors; comparing the relative weights of key indicators in Taiwan; comparing the cognitive evaluation of environmental factors perceived by university professors at four different types of universities in Taiwan; and comparing the cognitive evaluation of environmental factors perceived by university professors in Taiwan.