The evaluation research of enterprise innovation efficiency has been a focus of academic attention, but the construction of the evaluation index system of enterprise innovation efficiency are carried out mostly by the absolute number of the resource input index and technology output index, while it is lack of research based on the relative number of the input and output index reflecting the achievements quality of science and technology. Therefore, based on the 2011-2013 525 Nanjing's high-tech enterprises date and through two kinds of evaluation index system, this paper uses difference analysis, feasibility analysis and practical analysis to verify the scientific nature of the evaluation index system of enterprise innovation efficiency, which is in the perspective of achievements quality.