This paper presents a new hybrid power system with battery depth-of-discharge (DOD) management for extending battery cycle life and system service time. The proposed power system consists of a power management system, a dual-battery unit, a fuel cell (FC) stack, and two dc/dc unidirectional power converters. The dual-battery unit serves as the primary power source, while the FC stack serves as the secondary power source. The proposed power management is based on a state-machine-based mechanism, using a battery interchanging strategy to limit batteries operating within a given DOD range. The state-machine-based mechanism is employed for reducing the effects of battery overcharging or overdischarging; thus, it can significantly improve the battery life time. In addition, this algorithm has the ability to distribute the power flow efficiently between the dual batteries and the FC stack, and also to keep providing a stable and continuous energy output for the load. A current-mode control dc/dc boost converter is designed to regulate the FC current and try to maximize the FC power for battery charging time reduction. The proposed hybrid system introduced in this paper is designed and implemented with a 20W proton exchange membrane fuel cell (PEMFC) stack and two 12Ah lithium iron phosphate (LiFeP04) batteries. The experimental results of capacity fades on various DOD tests verify the usefulness of the proposed fuel cell/dual batteries hybrid power system. The comparison of life improvement is also shown in test results.