Faced with the challenge of globalization, higher education expansion, and marketization, the governance of higher education has changed to deregulate control and devolve more autonomy to higher education institutions, to introduce market mechanism to encourage competition, and to emphasize accountability to control the quality of higher education. In the study it is found that the way the government in Taiwan has carried out higher education multi-track promotion system showed some patterns of the governance style which was mentioned above. The government formed a market mechanism by encouraging universities to compete for the funding of the multi-track promotion system, devolved more autonomy to universities by delegating the authority of teachers’ qualification reviews to them, and established accountability of universities. Therefore, the government examines how universities achieve the key performance indicators of implementing multi-track promotion system and decides whether to cut the funding of the relevant project if they didn’t achieve the indicators. The government hopes the strategies to promote the multi-track promotion system mentioned above can solve the problem that research has been valued over instruction in academia and the government can encourage universities to develop their distinctive features. The study reflected the influence caused by the way the government carried out higher education multi-track promotion system on the governance of the universities and academic professionalism as offering reference for the future policy development.