Abstract The use of alternative energy sources instead of HFO has been recognized as a promising way for reducing emissions from shipping and promoting the development of green shipping. However, it is usually difficult for the decision-making to select the best choice among multiple alternative marine fuels. In order to address this, a complete criteria system for sustainability assessment of alternative marine fuels was firstly established, and a fuzzy group multi-criteria decision making method has been developed to rank the alternative marine fuels by combining fuzzy logarithmic least squares and fuzzy TOPSIS (Technique for Order Performance by Similarity to Ideal Solution). Fuzzy logarithmic least squares method has been employed to determine the weights of the criteria for sustainability assessment, and fuzzy TOPSIS was employed to determine the sustainability order of the alternatives. An illustrative case with three alternative marine fuels including methanol, LNG and hydrogen has been studied by the proposed method, and hydrogen has been recognized as the most sustainable scenario, follows by LNG, and methanol in the descending order. The results show that the proposed method is feasible for prioritizing the alternative marine fuels; it also has the ability to help the decision-makers to select the most sustainable option among multiple marine fuels.