Abstract: To address the difficulty of directly comparing electrical energy storage and molecular energy pathways in material–energy networks across engineering scale, operating conditions, and end-use services, this study proposes a three-layer evaluation and scenario-adaptation method comprising functional positioning, engineering feasibility, and chain cost. Using 1 kW·h of surplus renewable electricity at the input side as a common accounting boundary, an evaluation framework is established based on conversion efficiency, the levelized cost of absorbed energy (LCCAE) of the project itself, and the unit input cost of the production–storage–transport chain excluding electricity purchase costs. The method first screens feasible storage options according to functional positioning, inventory scale, project scale, and infrastructure conditions, and then compares the production–storage–transport costs within candidate sets providing equivalent end-use services. Using representative engineering parameters and a baseline transport distance of 1, 000 km, for a 5 h inventory period, hydrogen, ammonia, and methanol pathways are respectively matched with salt-cavern hydrogen storage (where salt-cavern resources are available and a minimum capacity of 100 t-H₂ is constructed) or high-pressure hydrogen tanks (where such resources are unavailable), pressurized ammonia storage, and atmospheric methanol tanks. The corresponding unit input costs are 0.104 or 0.166, 0.146, and 0.144 CNY/(kW·h), respectively. Furthermore, inventory thresholds are converted into annual production and delivery scales, providing a basis for the forward-looking deployment of large-scale storage facilities. The proposed method offers a quantitative basis for pathway screening and network planning under specified end-use demands, inventory requirements, and infrastructure conditions.