Nonprofit organizations have significant effects and functions in our society. It is an important part of social system. The performance evaluation of nonprofit organizations is essential in order to help the organizations developed well. With the development of performance appraisal, evaluating performance in nonprofit organization became a basic part of it. Researches fund that performance evaluation in nonprofit organization combination method of quantitative, qualitative, and process. This article based on the situations of nonprofit organization in China, shows the standards and methods in performance evaluation in nonprofit organizations, analyzes the problems and difficulties during the appraisal, and find out some measures to deal with the problems.