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Tropical rainforests in the central hilly section of Hainan Island are the source of the Nandu, Changhua, and Wanquan rivers, which are crucial for water conservation and ecological protection. The quantitative assessment of water yield in the three basins is beneficial for developing regional water resource protection plans, establishing ecological compensation mechanisms, and maintaining ecological balance. Based on land use data from five periods between 1980 and 2020, this paper adopts the InVEST model and geographic detectors to investigate the spatial-temporal variation characteristics and driving factors of water yield in three major basins of Hainan Island. The results demonstrate that forestland, which makes up more than 70% of the total area in the three basins of Hainan Island, is the predominant land use type. With a depth of 1269.18 mm, Wanquan Basin is the deepest of the three basins, followed by Nandu Basin and Changhua Basin. The total water yield of three basins shows a slightly decreasing trend from 17.991 billion m3 in 1980 to 17.864 billion m3 in 2020. The spatial distribution of water yield is high in the southeast region and low in the northwest region, with strong autocorrelation and significant aggregation. According to geographic detection, land use type is the dominant factor for the spatial differentiation of water yield in the three basins, with a contribution rate of 0.563, and soil type and annual precipitation are important impact factors. The interaction and synergy of soil types and land use types jointly affect the spatial differentiation of water yield in the basin. The results of this study can provide data support and scientific references for biodiversity conservation and ecosystem restoration in the three major basins of Hainan Island.