Hydrogen-based multi-microgrid systems (HBMMSs) are beneficial for energy saving and emission reductions. However, the optimal sizing of HBMMSs lacks a practical configuration optimization model and a reasonable solution method. To address these problems, we designed a novel structure of HBMMSs that combines conventional energy, renewable energy, and a hydrogen energy subsystem. Then, we established a bi-level multi-objective capacity optimization model while considering electricity market trading and different hydrogen production strategies. The objective of the inner model, which is the minimum annual operation cost, and the three objectives of the outer model, which are the minimum total annual cost (TAC); the annual carbon emission (ACE); and the maximum self-sufficiency rate (SSR), are researched simultaneously. To solve the above optimization model, a two-stage solution method, which considers the conflicts between objectives and the objectivity of objective weights, is proposed. Finally, a case study is performed. The results show that when green hydrogen production strategies are adopted, the three objectives of the best configuration optimization scheme are USD 404.987 million, 1.106 million tons, and 0.486, respectively.