Abstract:Taking 354 listed companies on GEM as the sample, this paper evaluates the technical efficiency of enterprise innovation from the perspective of heterogeneous industry by Polarization modeling and DEA secondary superposition, and reveals the innovation efficiency distribution of the listed companies on GEM. the conclusions are as follows: (1) That the improving DEA method by Polarization modeling and DEA secondary superposition is used to measure the enterprise comparable innovation efficiency of heterogeneous industry is effective; (2) Three quarters of the comparable innovation efficiency of the listed companies on GEM are less than 0.4, and there is a big space for improvement; (3) In terms of the average comparable comprehensive innovation technology efficiency, the most are the broadcast industry, TV industry, film industry, and video and radio production; the next are software and information service industry; the lowest are computer, communications and other electronic equipment manufacturing industry; (4) The results also shows there are larger imbalance in structure of enterprise innovation investment, and the effectiveness of the R D input have not been released efficiently. And, it’s more effective to promote innovation efficiency by improvement of management, motivation, and technology than altering the scale simply.