The study of island development suitability can provide important reference for island ecosystem-based management and sustainable development, as well as technical foundation for land development suitability evaluation and spatial planning in other areas. In this study, two typical China's archipelagos, namely, Miaodao Archipelago and Dongtou Archipelago, were selected to demonstrate the study. The carrying capacities of the three major development types, that is, ecological conservation, agricultural production, and urban construction, served as basic data; the controlling factors of island development suitability were identified in aspects of terrain, sea, and soil, and their influences on the three development types were separately measured in the two archipelagos and on different types of islands; and the island development suitability index (IDSI) was established for each of the three development types. Then, four schemes, namely, Schemes A-D, were designed based on the IDSIs and for purposes of free development, ecological conservation, agricultural production, and coordinated development, respectively, to conduct the island functional zoning, and the optimum scheme was finally selected. The results indicated that the influence natures and degrees of controlling factors showed distinct spatial heterogeneities across different archipelagos and across different types of islands within the same archipelago. Area proportions of the planned zones varied in different schemes for different purposes, and the optimum scheme was generated by assigning Schemes A, B, C, and D to the reclamation areas within the islands, the uninhabited islands, the sandy island, and the remaining islands, respectively. The present study validated two hypotheses: First, the factual influences of controlling factors on the land development suitability varied across different areas and might not be in accordance with the empirical cognitions. Second, the method of multiple schemes for different development purposes could contribute to solving the problem of disconnection of land development suitability with spatial planning.