Abstract: To further deepen the reform of scientific research institutions and establish a modern scientific institution system with“clear responsibility, scientific evaluation, orderly opening, standardized management” as soon as possible, focusing on the comprehensive evaluation without clearly goals, an evaluation system was put forward according to the orientation and responsibility of agricultural scientific research experiment base under the new situations. The system management software was designed and developed using fuzzy evaluation theory and database construction technology to realize workflow management, evaluating index management and reported data management in the performance evaluation process. And thus the functions of the evaluation system including performance evaluation, score calculation, data statistics and result publication were achieved. Then the system was applied to the experiment base of Xinjiang Academy of Agricultural Sciences. The evaluation results were in accordance with the actual situation and could reveal its position and contribution portion in all the experiment bases of Xinjiang Academy of Agricultural Sciences. This evaluation system provided a scientific basis for appraisal work in Xinjiang Academy of Agricultural Sciences, laid a foundation for the calculation of performance related pay, and offered a scientific method for the evaluation of management and development capability of agricultural scientific research experiment bases in China.