Based on the penetration drive of digital economy to factor marketization allocation in science and innovation industry, digital empowerment is of great significance to integrate the evaluation index system of factor marketization allocation in science and innovation industry. This paper measures the factor marketization allocation of science and innovation industry in each Chinese province from 2011 to 2020, and analyzes its dynamic evolution process. The outcome shows that the overall level of the index is not high, though it is in slow growth year by year. The index demonstrates a decreasee from the Eastern to the Middle, and to the Western economic regions. Moreover, there are obvious spatial differences and decentralized characteristics in the allocation. The typology of the index in each province is relatively stable; however, there are still significant differences in the probability of type shifts in different contexts. This paper provides empirical evidence and practical guidelines for identifying the development stages of science and technology innovation industry and breaking through the development bottlenecks.