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In the context of China’s implementation of innovation-driven development strategy and the comprehensive construction of “double first-class” colleges and universities in the new era, economy and culture after the COVID-19 epidemic, in order to scientifically and effectively evaluate China’s higher education innovation efficiency, This study employs the DEA-Malmquist index approach, which is based on the panel data encompassing 30 provinces and cities in China, spanning the years 2012 to 2021., and conducts static and dynamic analysis. The results of the study show that:1. China’s higher education innovation efficiency fluctuates and changes from 2012 to 2021, with an overall decreasing trend, and the imbalance in the development of higher education innovation among regions is an important reason for this change. 2. The total factor production index of the three regions in the east, centre and west all have a smaller degree of decline, and the overall innovation efficiency of higher education in the eastern region surpasses that of the central and western regions, the economic level and the support of resource inputs are the main reasons to make the higher education innovation in the east maintain a better efficiency. 3. The reasons for the low total factor productivity in each province and city are different, but on the whole, the progress of innovation in China’s higher education institutions is now mainly dependent on the improvement of technological efficiency.
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