As an important form of technological innovation, the collaborative innovation of industry-university-research institute has attracted more and more attention from the business circles, science and technology management departments and academic circles in China. Against this background, the performance evaluation model of industry-university-research collaboration innovation was established on the basis of the input-output perspective, and the factor analysis was used to scientifically assess the performance of industry-university-research collaboration innovation in 29 provinces and cities in China. The scores and rankings were analyzed in detail.