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An energy system with desalination and hydrogen production and storage is a promising option for remote areas with shorelines, e.g., Middle East, to jointly manage electricity, desalinated water and hydrogen resources. Thus, a hybrid renewable energy system considering seawater reverse osmosis desalination, proton exchange membrane electrolyzer stacks, and also proton exchange membrane fuel cell, is proposed. This work focuses on the optimal operation problem of the system. It is established in a multi-objective optimization manner, with consideration of minimizing system total cost, power transmission and renewable energy curtailment. The problem is solved with Non-dominated Sorting Genetic Algorithm-III, a meta-heuristic method dedicated to multi-objective optimization. Results show through the solving of the optimization problem the optimal energy management strategy can be obtained, and in the studied scenario, the system can avoid 38–42% of carbon dioxide emission compared to conventional electricity generation and gray hydrogen production measures. The operational benefit of fuel cell is also verified. Compared to existing works, this work maintains the flexibility and cleanness of green hydrogen production components, consider more aspect in operation and can be solved with limited computational resources and obtain a satisfying result. [ABSTRACT FROM AUTHOR]