Salaries and bonuses management is one of important topics in human resource management that plays an important role in productivity, efficiency and effectiveness of human force in organization. Compensation systems are established for managing salaries and bonuses. They can also improve staff satisfaction. These systems can provide and environment for implementation and evaluation of organization’s strategies. Designing of compensation system with considering organization’s strategies, especially human resource strategies, can improve human resource management. This system can help with achieving organization’s goals. The main goal of this thesis is to design a compensation system that considers human resource strategies. This efficient system can manage salaries and bonuses based on deferent indexes. In the first stage, we provided a method for estimating salaries based on economic stratums. In second stage, we computed bonuses by using human resource strategies and multi criteria decision making (MCDM) methods. In next stage, we used cafeteria package method for identifying facilities. For evaluating result of the system, we established it in one deputy of Esfahan's municipality for 3 month. The results show that increase in salary in this system is related to achieving strategic goals and job promotion. Post meetings with managers show that they are satisfied with results of the system. Also there was satisfaction between staff. These feedbacks showed us the efficiency of designed compensation system.