This study aims to evaluate the patterns of program cooperation among cross-strait universities for promoting mutual development. This study collected the data related to the current cross-strait university cooperation and exchange programs. Fifty-eight leading universities have been reviewed by using their numbers of ongoing cooperation and exchange programs in their official web pages. The target group has been reviewed, which includes 31 universities in Taiwan and 27 universities in mainland China. This study transformed the data by applying mean, t-test, and cluster analysis for further interpretation. The result reveals the cooperation differences among the universities by sectors and their locations. According to Euclidean distances, three significant clusters among the universities have been found. The different patterns of linkage among the universities provide more meaningful implications for university cooperation. Moreover, the SWOT analysis provides further information to interpret the selection of strategies among the cross-strait universities to enhance their cooperation. Finally, this study proposes some suggestions for researchers to expand knowledge in this issue.