Based on the developing status and different modes of educational exchange and cooperation between Fujian Medical University (FJMU) and universities in Taiwan in recent years, this paper analyzes the existing problems during the exchanges and cooperation, such as small scale, narrow field, and vulnerability to regulations’ and policies’ impacts. Possible methods and measures that could be taken will be discussed and explored, such as expansion in exchange scale, development of joint educational as well as scientific research programs, and establishment of a regular exchange mechanism, so as to further develop and promote the exchanges and cooperation between FJMU and universities in Taiwan.