With the deepening of China's innovation system reform entering into the 21st century, its functionality has received considerable attention in both academic and policy-making contexts. However, it has not been fully uncovered yet in a more systematic and practical manner possibly due to theoretical or methodological reasons. In this study, a structural approach with partial least squares is introduced to incorporate various functional constructs together determining the performance of innovation systems into an integrated path framework based on the extended framework of Romer's idea production function. By constructing a rich province–year panel dataset over the 10th five-year plan period of China, we use the novel analytical framework to detect and untangle the periodically operating state of China's regional innovation systems (RISs) in terms of the effectiveness of functional constructs shaping and influencing the innovation process. The examination results show that China's RISs perform well in terms of the performance of most functional constructs except for “innovation linkage” as well as “innovation sophistication”. With respect to the interactive effects between the contextual innovation environment and the innovation process, however, China's RISs perform poorly from the perspective of system thinking. ►The paper provides new insights into development of research in China's regional innovation systems. ►The heart of the contribution is indeed the use of a structural approach that enables to uncover and quantify the performance of China's regional innovation. ►The paper contributes to theoretical or methodological progress to measure performance of regional innovation systems and provides new evidences to China's RISs.