Improving green innovation efficiency is important to promote green economic development， but the spatial misallocation of innovation resources seriously inhibits efficiency improvement. Under the wave of digitalization， it is significant to explore whether the digital economy can promote urban green innovation efficiency by improving the spatial misallocation of innovation resources. Based on the panel data of 282 prefectures or higher-level cities from 2006 to 2022， it built the system GMM model to examine the empirical questions. The results show that China is generally under-allocated in terms of innovative human resources and over-allocated in terms of R&D capital； and by region， cities in the east are under-allocated and cities in the west and northeast are over-allocated. The digital economy can alleviate the spatial misallocation of innovation resources， thereby improving green innovation efficiency. Further studies find that there are regional and city-level differences in the impact of digital economy on the spatial misallocation of innovation resources and their green innovation efficiency， and differences in the direction of the spatial misallocation of innovation resources also affect results. From the digital economy perspective， it provides theoretical support and policy suggestions for optimizing the spatial allocation of innovation resources and improving urban green innovation efficiency.