The Aral Sea was the fourth largest lake in the world but it has shrunk dramatically as a result of irrational human activities, triggering the “Aral Sea ecological crisis”. The ecological problems of the Aral Sea have attracted widespread attention, and the alleviation of the Aral Sea ecological crisis has reached a consensus among the five Central Asian countries (Kazakhstan, Uzbekistan, Tajikistan, Kyrgyzstan, and Turkmenistan). In the past decades, many ecological management measures have been implemented for the ecological restoration of the Aral Sea. However, due to the lack of regional planning and zoning, the results are not ideal. In this study, we mapped the ecological zoning of the Aral Sea from the perspective of ecological restoration based on soil type, soil salinity, surface water, groundwater table, Normalized Difference Vegetation Index (NDVI), land cover, and aerosol optical depth (AOD) data. Soil salinization and salt dust are the most prominent ecological problems in the Aral Sea. The Aral Sea was divided into seven first-level ecological restoration subregions (North Aral Sea catchment area in the downstream of the Syr Darya River (Subregion I); artificial flood overflow areas downstream of the Aral Sea (Subregion II); physical/chemical remediation area of the salt dust source area in the eastern part of the South Aral Sea (Subregion III); physical/chemical remediation areas of severe salinization in the central part of the South Aral Sea (Subregion IV); existing water surface and potential restoration areas of the South Aral Sea (Subregion V); Aral Sea vegetation natural recovery area (Subregion VI); and vegetation planting areas with light salinity in the South Aral Sea (Subregion VII)) and 14 second-level ecological restoration subregions according to the ecological zoning principles. Implementable measures are proposed for each ecological restoration subregion. For Subregion I and Subregion II with lower elevations, artificial flooding should be carried out to restore the surface of the Aral Sea. Subregion III and Subregion IV have severe soil salinization, making it difficult for vegetation to grow. In these subregions, it is recommended to cover and pave the areas with green biomatrix coverings and environmentally sustainable bonding materials. In Subregion V located in the central and western parts of the South Aral Sea, surface water recharge should be increased to ensure that this subregion can maintain normal water levels. In Subregion VI and Subregion VII where natural conditions are suitable for vegetation growth, measures such as afforestation and buffer zones should be implemented to protect vegetation. This study could provide a reference basis for future comprehensive ecological management and restoration of the Aral Sea.