Existing innovation evaluation methods have the problem of 'emphasizing output rather than application', which leads to enterprises 'emphasizing quantity rather than quality', even false innovation behavior. And the non-technological innovation is ingored. Therefore, it is urgently necessary to research a scientific and perfect evaluation system of innovation. The internal mechanism of innovation activities is analyzed based on innovation value chain. An innovation evaluation model is constructed，which is consisted of knowledge innovation, factor innovation and innovation implementation. And also an open three-stage innovation evaluation index framework is designed. And then the whole process and elements of enterprise innovation activities could be evaluated stage-by-stage. Thereby enterprises is guided to all-around and substantive innovation.