With the aggravation of global environmental pollution problems and the need for energy restructuring, hydrogen energy, as a highly clean resource, has gradually become a hot spot for research in countries around the world. Facing the requirement of distributed hydrogen in refueling the original station for hydrogen transportation and other usage, this paper proposes a comprehensive energy system planning model for hydrogen refueling stations to obtain the necessary devices construction, the devices’ capacity decisions, and the optimal operation behaviors of each device. Comparing to traditional single hydrogen producing technics in the traditional planning model, the proposed model in this paper integrates both water-electrolysis-based and methanol-based manufacturing technics. A two-level optimization model is designed for this comprehensive system. The result of the numerical study shows that the proposed model can achieve a better optimal solution for distributed hydrogen production. Also, it considers the single producing situation when price of one primary resource is sufficient higher than the other.