A fuel cell/secondary battery hybrid power generation system could extend well beyond the efficiency and interoperability of the conventional diesel generator. The suggested power source system consists of 2.3 kW class PEMFC, 100 Ah lithium polymer battery, and two DC/DC converters by serial connection type. It was known that interoperability of sub-systems is the key factor for stable and optimal control of the hybrid power generation system. The modeling and simulation methods have been proposed to reduce the number of configurations and performance tests for components selection and select the optimized control condition of the power generation system. The control model for power source system is implemented based on the empirical formulation and carried out in the Matlab/Simulink environment. The results show that the simulation can be used to establish the algorism of prototype and increase the durability of the power source system.