Abstract:As a kind of open innovation mode, collaborative innovation in universities is widely used in solving all kinds of research and development problems. Based on the dynamic capability theory, this paper constructs the collaborative innovation input-output-transformation process model,establishes the corresponding evaluation index system to evaluate collaborative innovation capability and efficiency of C9 league colleges, so as to provide universities with reference of collaborative innovation management practice. The empirical results show that: first, collaborative innovation abilities of C9 league colleges is highly differentiated,the difference of input, output and transformation at the later stage is greater ,the overall strength of Tsinghua University, Shanghai Jiaotong University and Zhejiang University is strong. Second, regarding to collaborative innovation efficiency of input-output, output-transformation and transformation-input, most of universities have higher collaborative innovation input-output level, but have lower efficiency of output-transformation and transformation-input, the overall system performs poorly.