The spatial selection of desalination water intake is affected by many factors such as natural geography, ecological environment, and social economy, which determines the economy, stability, and safety of desalination engineering construction. Based on the analysis of influencing factors of seawater desalination intake site selection for shallow water intake mode, the representative evaluation indexes of seawater desalination intake are selected by considering basic geographical conditions, seawater environment conditions, disaster conditions, and industrial development conditions. Then we constructed the suitability evaluation model of seawater desalination intake site selection. Taking the coastal waters of the Rongcheng City, Shandong Province as the study area, based on the multi-factor spatial overlay analysis and operation of GIS platform, this study built the preliminary suitability spatial zoning. This, combined with superimposing constraints, generated the final results of seawater desalination intake site selection suitability spatial zoning, and thereby formed a scientific, quantitative and spatial evaluation system of seawater desalination intake suitability. This study improves the existing method of seawater desalination intake site selection on the theoretical and technical level, and the evaluation results provide a scientific basis for seawater desalination intake site selection.