A “virtual enterprise” is an effective organization formed by enterprises and partners under market opportunity which can flexibly adapt to the dynamic market demand and improve the competitiveness of enterprises. To select virtual enterprise partners objectively and scientifically, this study proposes the evaluation model of the innovation resource capability of the alternative enterprises under the unknown weight. In the multigranularity hesitation fuzzy language environment, the unknown weight is solved by using fuzzy entropy theory. The risk attitude of decision-making enterprises is introduced by using the improved prospect theory and the selection of partners is comprehensively considered. Finally, a case study is presented to demonstrate the effectiveness of the proposed approach. The research intends to enable the virtual enterprise to choose the partners swiftly such that they can compensate for the shortcomings and optimize the allocation of innovation resources.