Global decarbonization trends encouraged the consideration of a methane hydrate (MH) development system design combined with carbon capture and storage (CCS) in the Japanese national MH research program. Previous studies have also proposed decarbonized MH development systems, but the conclusions vary due to epistemic uncertainty. Epistemic uncertainty arises from the knowledge and understanding of the subject, and each expert has different assumptions. Therefore, we assume that developing a model encompassing epistemic uncertainty as a platform allows for discussion toward system design decisions. This study builds the evaluation model, considering epistemic uncertainty to support the decision-making on the system design and reveal the tradeoff. It identifies the epistemic uncertainty affecting the tradeoff by changing the conditions based on previous studies. The evaluation model consists of technological options as modules, and all system concepts are evaluated by combining them. Epistemic uncertainty was subdivided and implemented within the evaluation model. As a result, the evaluation model output the tradeoff with bands of uncertainty. While the development field significantly impacts the results, hydrogen-related systems and offshore power plant systems score well owing to synergies between options. The epistemic uncertainty analysis regarding the tradeoff suggests that system design uncertainty impacts the conclusions. This finding indicates the importance of the model development as a platform for the evaluation of various system designs. This study contributed to an approach to model-based decision-making with epistemic uncertainty.