Taking the innovation efficiency evaluation as the breakthrough point, this paper mainly analyzes the selection of core indicators of innovation efficiency evaluation of enterprise R & D institution in different industries. The research finds: the setting of the efficiency evaluation index system has a direct impact on the final evaluation results of R & D institutions in different industries, and the human resource indicators like highly educated personnel have a greater impact on the efficiency of labor intensive industries; the financial and material resource indicators like expenditure have a greater impact on the efficiency of capital intensive industries; the innovation achievement indicators like effective invention patents have a greater impact on the efficiency of technology intensive industries; the economic efficiency indicators have significantly impact on all of the three major categories of industry.