Abstract: Based on Guangdong Province－Ministry University－Industry collaborative project, the effect of ownership of enterprises on the performance of cooperation Innovation for Industry-University-Research in the three phases of the innovation value chain has been explored in this paper. The results show that there is no significant difference of performance between SOE and other kinds of enterprises in the phase of knowledge innovation. The performance of POE is significantly higher than that of SOE in the phase of science and research innovation. There are significant differences of performance in the phase of product innovation and the performance of MOE is significantly higher than that of SOE with respect of achievements of transformation. The performance of HMT is significantly higher than that of SOE with respect of achievements of new product, new process and achievements of transformation. The performance of FIE is significantly higher than that of SOE with respect of new process and achievements of transformation.