The three major basins of Hainan Island serve as both biological barrier zones and vital resources of water conservation for the entire island. In recent years, there have been significant land use changes in the basins, making the local ecosystem more fragile. Landscape ecological risk assessment conducted in the three major basins is critical for improving regional ecological security and promoting sustainable development and utilization. Taking Nandu River, Changhua River, and Wanquan River in Hainan Island as the study area, this study utilized methods such as landscape ecology and geographic detectors to explore the spatiotemporal changes in landscape ecological risks and the driving factors for the three major basins from 1980 to 2020. The findings indicate that: (1) Forest and arable land make up the majority of land use types in the three major basins. During the 40 years, land use changes can be primarily reflected by the continuous increase of construction land and water area and the continuous decrease of arable land and grassland area. The changes in the three basins' landscape patterns indicate a strengthening of landscape fragmentation and diversity as well as a weakening of landscape connectivity. (2) The landscape ecological risks in the three major basins have been relatively stable over the past 40 years. The risk index is primarily low or moderately low, covering more than 70% of the overall basin area. (3) The three major basins exhibit a declining tendency in the spatial clustering of landscape ecological risks, mostly displaying a "high-high" and "low-low" pattern. High-risk areas are concentrated in the northeast of the three basins, whereas low-risk areas are located in the National Park of Hainan Tropical Rainforest upstream of the basins. (4) Land use intensity is the main driving factor affecting the spatial differences of landscape ecological risks in the three major basins. With an explanatory power of 64.7%, the interaction between land use intensity and slope is the primary cause of the spatial differentiation of landscape ecological risks. The findings of this study can serve as valuable resources for the landscape ecological optimization and governance of the Hainan Island basins.