In view of the problems in scientific research management in colleges, this paper proposed a kind of regional collaborative innovation mode which was superior to the traditional mode based on the long-term scientific research management practice of a certain college which belongs to the “985” project university, and taking into consideration the regional collaborative innovation systems theory. The analysis of each scientific performance indicator from 2002 to 2011 showed that all the indicators increased steadily. With the transition from quantification assessment to fuzzy assessment, the rapid growth trend of scientific performance slowed down. However, scientific performance indicators improved, according to the results of International Assessment and China Discipline Ranking of the Ministry of Education. This paper provided policy suggestions for further improvement of scientific research performance.