The selection of partners for enterprise is a multi-attribute decision-making process with timing and fuzzy information. The decision-making method is established by combining orthogonal projection, time degree and intuitionistic fuzzy multi-attribute decision-making theory, the capability field model of partner selection was constructed based on collaborative innovation capability, and the process of partner selection for enterprise innovation ecology was designed to select and eliminate partner enterprises. Finally, the effectiveness and superiority of this method are verified by an example.