The goal of this study was to reveal the mechanism of the Chinese industry-university-research collaborative innovation (IURCI) and interactions between the elements in the system and find issues that exist in the collaborative innovation process. Based on the theoretical perspective of innovation and complexity science, we summarized the elements of the IURCI as innovation capability, research and development (R&D) configuration, and knowledge transfer and established a theoretical model to describe the evolution of the IURCI system. We used simulation technology to determine the interactions among variables and the evolution trend of the system. The results showed that the R&D configuration can promote the evolution of innovation capability and knowledge transfer and that innovation capacity is the current dominant factor in the evolution of the Chinese IURCI system and is highly positively correlated with R&D configuration. The evolutionary trend of knowledge transfer was gentler, and its contribution to the evolution of the Chinese IURCI system was less than that of R&D configuration. When innovation, R&D configuration, and knowledge transfer are relatively balanced, the collaborative innovation system can achieve high speed and stable evolution.
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