Abstract: Under the background of “Double First-Class” construction, optimizing the allocation of higher education resources to improve the efficiency of input and output is an important issue in the development of higher education. This paper uses the DEA model to evaluate the scientific and technological innovation resource allocation efficiency of 31 provinces in China from 2015 to 2017, and calculates the output shortage of each province in 2017. The results show that the structure of science and technology innovation resource allocation in universities in some provinces is unreasonable; the efficiency of science and technology innovation resource allocation in universities in the three major regions is western region, central region and eastern region in order from high to low; the overall technical efficiency changes with pure technical efficiency in western and central regions, the overall technical efficiency changes with scale efficiency in the eastern region; pure technical efficiency plays a key role in the overall technical efficiency. In order to improve the efficiency of the allocation of scientific and technological innovation resources in Chinese universities, we should improve the policy system construction from the macro level; strengthen the integration of social resources from the meso level; and optimize the internal allocation of universities from the micro level.