Innovation enterprise is a new enterprise operation and development form and it has strong continuous innovation ability and can active enterprise positivism and creativity. Constructing innovation enterprise appraisal index system is helpful for enterprise to be the true main body and assure enterprise to develop fast, healthily and soundly. The paper is on the basis of summing up the definition and analyzing the construction factors of innovation enterprise and builds the appraisal index system from the four angels of technology, products, marketing and management and it also gives appraisal standard and an applied appraisal method.