Abstract: In order to evaluate collaborative innovation abilities of Xiamen, Zhangzhou and Quanzhou, an evaluation index system was constructed, the collaborative innovation abilities of three cities and the gaining benefits from collaborative innovation were analyzed respectively with Principal Component Analysis and Competence Structures Relational Models. The results showed that in order to improve the collaborative innovation relationship among three cities, we should promote free flowing of innovation resources among cities, and increase the radiation range of Xiamen and Quanzhou on Zhangzhou; establish new mechanism of urban collaborative innovation; complement the industry chains in Xiamen, Zhangzhou and Quanzhou, which was of great significance to optimize the innovative resources allocation between cities.