Views from the advanced countries, universities, due to the intervention of market forces, are subjected to changes in the nature and the function, compete for funding for such subsidies, and face the multiple competitive pressures and difficulties which lead to governments’ and universities’ challenges to transition management. Among the models of transition management, Etzkowitz’s three triple helix model is widely accepted by States, which promotes universities, industries and governments to work closely in order to drive the countries' overall economic development. The interaction of the three universities, industries and governments, can grow and become more and more equal relationship that could lay the cornerstone for long-term cooperation among them. The development of higher education in Taiwan also faces the same problems above. Basically, this paper, based on Etzkowitz’s three triple helix model, is to explore how universities conduct the transition management as the by Etzkowitz’s three triple helix model’s the implications and analysis of the relevant literatures. The paper is also to research universities’ transition management and to induce the directions of universities’ future transition management I; finially, the researcher would made conclusions as the references for universities’ transition management.