This paper uses the DEA model to study the allocation efficiency of the eastern region innovation resources, the results of the study show that the eastern region has 6 provinces and innovation resource allocation efficiency is higher, but there are still 5 provinces and the efficiency is not high, there are different degrees of innovation input redundant or insufficient output. This put forward that various provinces and cities should make the most of the advantages of location and resources based on the continuous optimization of innovation resources allocation efficiency; individual provinces and cities should accurately grasp the advantages and disadvantages to optimize the allocation of innovation resources efficiency, so that the innovation of the eastern region can drive development of itself and lead to the development of the central and western regions in the economic transformation period.