Abstract The paper constructs the evaluation index system for performance of regional science and technology synergy innovation. On the basis of multi hierarchy and index value of the fuzzy and random characteristics, it puts forward the model of regional science and technology synergy innovation performance evaluation based on cloud theory. By selecting the 31 provincial-level administrative regions, empirical study shows that performance of China’s regional science and technology synergy innovation is still at a low level and presents the hierarchical characteristics. Finally, we discuss the main problem found and put forward the corresponding policy recommendations.