Abstract: Current marine spatial planning predominantly focuses on a two-dimensional horizontal approach and lacks scientific methods for three-dimensional (3D) sea-use planning. To more efficiently unlock the potential of marine resources and alleviate spatial conflicts, this study constructed a 3D quantitative marine spatial planning model that integrates compatibility analysis and suitability evaluation, based on a four-layer spatial division of “water surface-water column-seabed-subsoil”. The model firstly quantifies the spatial compatibility among 20 major sea-use activities using a conflict coefficient matrix, effectively identifying and avoiding incompatible combinations. Subsequently, a suitability evaluation indicator system was developed for different marine spatial layers, focusing on typical sea-use types such as offshore wind power, offshore photovoltaic, tourism, and port construction on the water surface layer, aquaculture in the water column, and seabed aquaculture. Using GIS-based overlay analysis and the analytic hierarchy process, suitable zones for various marine activities were identified. Based on the compatibility analysis and suitability evaluation results, the study further selected marine activities with high compatibility and large overlapping areas suitable for optimized vertical and horizontal spatial allocation. Finally, by integrating the practical development conditions of regional marine industries, appropriate three-dimensional and multi-layered sea-use patterns of the target region, the model proposes locally appropriate 3D hierarchical sea-use patterns and optimization suggestions for spatial planning layout. This study provides a practical demonstration and technical support for implementing 3D sea-use spatial planning in coastal regions.