The maritime industry is moving towards a sustainable supply chain (SSC), intending to increase the quality of logistics and make more profit. The sustainability of the maritime supply chain (MSC) in Iran is one of the topics that has not been widely studied. Ports play a crucial role in promoting Iran’s position in the international transit of products, strengthening economic, social, and environmental connections with neighboring eastern and northeastern countries, improving GDP, and promoting the role of the free zone in the national development of the country. Port development is one of the essential elements in the government’s strategic planning in developing and activating the East axis. It has a special priority in line with government policies based on deprivation elimination and improving people’s living standards. This paper considers five significant ports of Iran that are part of special economic zones and studies the sustainability of those ports. In this research, different multi-criteria decision-making methods were applied to solve a sustainability-ranking problem of major Iranian ports. First of all, by using the SWARA method, sub-criteria of loading and unloading oil, pier length, and population obtained the highest scores in economic, environmental, and social aspects of sustainability, respectively, which shows that they had the greatest impact on the sustainability assessment of Iranian ports. Finally, the MARCOS and CoCoSo techniques were the most similar in all three dimensions of sustainability, and both seemed to be suitable methods for evaluating the sustainability of ports. Furthermore, the implementation of sensitivity analysis and definition of different scenarios for port evaluation and the high efficiency of the MARCOS method were determined in solving the port-ranking problem. According to the MARCOS method results, economic, environmental, and social criteria were all effective criteria in the sustainable development of major Iranian ports and have been largely applied in Astara, Bushehr, and Imam Khomeini ports. Based on the analysis of the results, several managerial insights to make better industry decisions are also revealed.