In case of residential fuel cell system, it is significant to stably supply heat and power to a house with high efficiency and low cost for the successful commercialization. In this paper, the control strategy analysis has been performed to minimize the total cost including capital and operating cost of the residential fuel cell system. The proposed analysis methodology is based on the simulator including the efficiency models as well as the cost data for fuel cell components. The load control strategy is the key factor to decide the system efficiency and thus the cost analysis is performed when the fuel cell system is operated for several different load control logics. Additionally, annual efficiency of the system based on the seasonal load data is calculated since system efficiency is changeable according to the electric and heat demand change. As a result, the hybrid load control combined electricity oriented control and heat oriented control has the most economical operation.