The coming of knowledge-based economy era brings up the creation and application of knowledge that become the sources of high technology competition. As technology process and the build of science park leads output value of high technology within the top ranks in the world. The focus of this study is to understand innovative mechanisms of university-industry cooperation between science parks in Taiwan and universities. It brings up suggestions by analyzing problems of innovative mechanisms of university-industry cooperation between science parks in Taiwan and universities. The study utilizes literature analysis, questionnaire investigation and semi-structured interview as the methods. There are 40 valid questionnaires via survey of university-industry cooperation staffs in universities, and the second is to interview there experts. At last, the study brings up some suggestions of innovative mechanisms of university-industry cooperation to universities and government.