It has been three years for the implementation of the total wage policy and the annual salary system in Sanming city Fujian province. This paper summarized the main results, including medical staff’s works were respected, hospital income structure was more standardized and top-down evaluation system was basically established. Then, we discovered the problems that hidden or had emerged during the execution of the process, including income stability of hospital staff could not be guaranteed, induced service problems were emerged, and salary design defects. Furthermore, we put forward some related suggestions to provide theoretical experience for the improvement of the salary system and the deepening of the reform of public hospitals.