Abstract—The performance evaluation of the enterprise is not only the effect of business, but also the basis of enterprise decision-making. What’s more, it is the baton which guides the direction of the employees’ work. China’s performance evaluation system of private enterprise is not reasonable and scientific, evaluation methods and evaluation index system do not real appraise scientifically on the enterprises’ independent innovation ability, couldn’t find and solve the deficiencies of the innovation ability through evaluation, and private enterprises couldn’t effectively guide and motivate the employees carry out independent innovation actively, which makes the capability of independent innovation of private enterprise weak relatively. Therefore, private enterprise should use some performance evaluation methods, such as Data Envelopment Analysis,to appraise the enterprise itself-periodically. Establishing the performance evaluation system of enterprise which considering the capability of independent innovation. In order to find and solve the problems of independent innovation of the private enterprise in time, and guide the employees to develop independent innovation initiatively. Promotingthe independent capability of private enterprise continuously improved.