The large amount of carbon emitted due to industrial development is posing serious climate change. Under these circumstances, hydrogen energy is being used as a major energy source and is attracting attention as an alternative energy to fossil fuels, characterized by high carbon emissions. While the use of hydrogen has the obvious benefit of a low carbon footprint, the hydrogen production process possesses a high carbon footprint difference depending on the source of utilized electricity. This study considers several situations arising in an electrolysis-based hydrogen supply chain network (HSCN). A multi-stage stochastic programming (SP) is modeled to consider the uncertainty of demand and transportation capacity generated in HSCN. Moreover, a typical stochastic model has a chain rule between the decision variables resulting from nonlinearity and uncertainty, and these features make it difficult to derive an effective solution. Thus, in this study, a new methodology, Weighted Scenario Sample Average Approximation (WSSAA), is proposed to derive an effective solution for the multistage SP model considering various scenarios under the hydrogen supply chain. While a general stochastic programming approach fails to generate feasible solutions with volatile HSCN uncertainties, the proposed WSSAA framework provides feasible decisions considering multiple scenarios. The effectiveness of the proposed model applied with WSSAA is demonstrated through comparative experiments over the models used in existing studies.