Abstract: The innovation efficiency of university research supports high-level scientific and technological development, and promotes the integrated development of education, science and technology, and talents. After measuring the innovation efficiency of university research using the super-efficient DEA-Malmquist method, the study evaluates the impact of China's higher education policy of merit-based support on the innovation efficiency of university research using the double-difference method in a quasi-natural experiment on the “Double First-Class” initiative. The study shows that the higher education meritocracy policy significantly improves innovation efficiency and passes a series of robustness tests. The reallocation of innovation resources and the spatial spillover effect of economies of scale are the important mechanisms, and the supported universities can improve the mismatch of innovation resources and the level of human capital. Heterogeneity analysis reveals that the higher education meritocracy policy will be more and more prominent if we can break down the institutional barriers and local protectionism. Even in regions that have not crossed the "middle-income trap" in terms of economic development or in regions with net population outflows, the integration of resources can still be promoted through merit-based higher education policies. In the future, the scientific research and innovation function of high-level institutions of higher education should be given full play to enhance the innovation efficiency of scientific research.