With the rapid development of technology, technology advancement is harder and harder with more and more risks in technology innovation, thus enterprises can’t carry out technology innovation program alone. The development of the emergence of the biotechnology industries provides valuable insights into the role of strategic alliances and networking that shaped the synergy between both industries. This paper provides a step by step methodology to evaluate R&D strategic alliances problem in Taiwan biotechnology Industry. The purpose of this paper is to formalize the choice of R&D strategic alliance modes for an individual multinational enterprise among Joint Venture, Franchise agreement, Licensing Agreement, Subcontract and Merger/acquisition. An illustrative example is presented to demonstrate the applicability of the proposed methodology. The proposed approach also provides a relatively simple and well suited decision making tool for this type of strategic decision making problem. This evaluation mode was identified as a workable method.