The current operation of China′s highway energy system heavily relies on the external power grid, with low penetration rates of renewable energy and huge carbon emissions. Therefore, a multi-stage planning method for comprehensive energy stations in highway service areas considering hydrogen energy is proposed. Firstly, a comprehensive energy station architecture that includes electricity, cold/hot, gas, and hydrogen energy is constructed to simulate the charging needs of clean energy vehicles within the highway service area. Based on the market ownership of hydrogen fuel cell vehicles in different periods, the planning cycle is divided into multiple stages, with the goal of minimizing total investment and operating costs. A multi-stage planning model for comprehensive energy stations in highway service areas considering hydrogen energy is constructed to determine the capacity configuration schemes for electricity, heating/cooling, gas, and hydrogen energy equipment, as well as operational strategies under different typical daily scenarios. Finally, based on the actual energy load data of a high-speed service area in northern China, it is verified that the proposed multi-stage planning model can effectively improve the economy of comprehensive energy stations and promote the consumption of renewable energy.