To establish an innovation alliance for national mega-projects is an effective and efficient way to enhance the capability of independent innovation. Considering the members have different backgrounds, this paper proposes the organizational characteristics as the influent factors of the weight setting, the intensity of which affects the weight process. The fuzzy AHP with triangular fuzzy number and linguistic variables are applied to pair-wise comparisons to evaluate the capability of each candidate. A case study is also given to demonstrate the potential of the approach.