This paper proposes an optimization planning method for weakly interconnected zero-carbon island chain microgrid clusters, aimed at green energy supply scenarios for island groups. The method constructs an island microgrid system based on photovoltaics, small wind turbines, electrochemical energy storage, and seawater desalination devices. Additionally, “freshwater-electricity” weak connections between islands are realized through electric speedboats. The entire model can be transformed into a bi-level planning model, where the upper level aims to maximize annual operational revenue, and the lower level aims to minimize the investment in seawater desalination facilities within the island chain. A case study of an actual island group in Eastern Malaysia demonstrates that the designed zero-carbon island chain microgrid planning not only provides reliable, environmentally friendly energy and freshwater supply to the island residents but also offers a good return on investment.