With the development of society and economy, our health care level has been greatly improved, while the size of the hospital is continually expanding. Reasonable, intelligent hospital performance evaluation mechanism plays an important role in the current hospital management. It not only can effectively help hospitals determine the future direction of development, but also help the hospital with the application of scientific methods for hospital staff assessment and evaluation to achieve a fair and impartial manner. In this study, the fuzzy neural network is introduced into the hospital performance evaluation, principles to maximize the performance of hospital performance indicators and create, and building hospital performance evaluation mechanism system. The basic framework of this system includes: operational capability, potential for development, the contribution of the staff for hospital and so on. Meanwhile, we take the attendance and medical safety as factors of evaluation hospital staff's performance. Because the staff and the judge is more often related to interest, reputation, etc, the application of performance evaluation mechanism based on fuzzy neural network can reduce the influence of subjective factors on the final results of the evaluation mechanism so as to be a fair and intelligent evaluation mechanism.