This paper constructs the evaluation model of structurel performance and functionl perform -ance based on the analysis of the meaning of entropy in regional innovation system.Under the two -dimensional framework of structure-function,this paper evaluates the performance of regional innova -tion system based on the panel data of 31 provinces in China from 2009 to 2017.Empirical research shows that the structure performance of China's regional innovation system shows a trend of high west and low east,the structure performance of innovation system in central and western regions is generally higher than that in eastern regions.The function performance of Beijing, Guangdong, Shanghai and Tianjin are still the first echelon，and the regional innovation system of Guangdong province has developed rapidly in recent years and its function performance ranks first in China.The function performance of Beijing and Shanghai regional innovation system has been declining in recent years. Under the two-dimensional framework of structure-function,this paper finds tha the structure performance and function performance of regional innovation system are negatively correlated,the improvement of function performance is often at the expense of structure performance,and the evolution process of regional innovation system has certain direction.The results expand the application range and depth of science of complexity in the regional innovation system，have important theoretical implications for regional cooperation and division of labor and the formulation of regional innovation policies.