While entering the WTO, Taiwan has become one of the members in the international community of globalization. The medium and small enterprises (M&SE), which account for 98 percent of Taiwan industries, are facing even more competition due to insufficient capital, human resources, and limited organization scale. To achieve competitive edges for the globalization requires efficiency in doing business and scale in industry development; meanwhile, M&SE should aggressively form strategic R&D alliances so as to effectively consolidate resources to jointly develop technical capabilities to multiply the synergy. In this paper, we propose a compromise optimization method called VIKOR, revised the popular TOPSIS technique, for solving multiple criteria decision making (MCDM) problems. To illustrate this procedure, we established a fuzzy analytic hierarchy process for evaluating the utility of an R&D consortium and then solve the optimal strategy assuming that the optimal compromise solution to comparing the synergy among proposed R&D consortia strategies. Through this research, we successfully demonstrate that VIKOR is a good assessment for evaluation of multiple criteria decision-making problems. Finally, we summarize some findings of this study and provide some suggestions for the development direction of M&SE in the near future.