With the increase of energy transformation and environmental protection awarenesses, fuel cells, as a clean and efficient energy conversion technology, have been widely adopted in transportation and stationary power supply applications. A single fuel cell has a limited power capability. On the other hand, the multiple fuel cells are combined into a multi-stack fuel cell system (MFCS), which provides a high power output and modular design. However, the energy management of such multi-stack systems faces challenges such as uneven power distribution, inconsistent stack life, and low overall efficiency. Current multi-stack fuel cell control systems often optimize single objectives, either efficiency or lifetime balance produce the optimized energy management strategy. This may not suffice for the overall system benefit. For example, if only efficiency is optimized by energy management, the failure to consider lifetime balance may result in uneven life degradation for each fuel cell, and vice versa. To address the above issues, this paper proposes an energy management strategy for multi-stack fuel cell systems that considers dual objectives, which can simultaneously ensure the optimal co-optimization of the output efficiency and stack life for each stack, thereby improving the overall operating efficiency and lifetime of the system. The effectiveness and practicality of the proposed energy management control strategy were verified on a 60kW dual-stack PEMFC fixed power generation system developed by SeeEx.