The polarization effect and diffusion effect of regional innovation in China have significant asymmetric impacts. That is to say, while absorbing innovation resources to form polarization effect, the feedback effect of innovation polarization region is very weak. It fails to form symmetrical diffusion effect on the output of innovation resources. This is also an important reason for the unbalanced development of regional economy in China. Therefore, China needs to break the geographical restrictions, to improve the technology undertaking environment in underdeveloped areas, to actively promote the industrial transfer between regions through investment attraction and to scientifically quantify the symmetry compensation amount of innovation resource output areas. Only in this way can we reach the final solution of the contradiction between the optimal allocation of innovation resources and the unbalanced development of regional economy.