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Seawater intrusion is a complex groundwater - seawater interaction process, and it is influenced by many factors from ground surface to underground, from groundwater to seawater. Generally, for seawater intrusion model, some model parameters and boundary conditions are always specified by model users’ personal experiences or literature's reference value. The defective model would damage the groundwater management for controlling and preventing seawater intrusion when making decisions are based on this model. In order to improve the reliability of seawater intrusion model, the influences of model inputs on output should be identified prior at optimizing model inputs.Dagu river basin, Jiaozhou Bay is one of the most serious areas of seawater intrusion in China, and it is chosen as the study area in this study. The seawater intrusion model of Dagu river basin is built based on a general program SEAWAT4. The key influence factors of model output are analyzed by two sensitivity analysis methods, i.e., stepwise regression and mutual entropy. The results demonstrated that the most important influence factors which have largest sensitivities to groundwater Cl- concentration are the precipitation rate and groundwater pumping in agriculture area. In addition, the hydraulic conductivity of zone 1 has a non-negligible influence on seawater intrusion process. Stepwise regression analysis is capable of identifying most important influence factor, and it can’t handle complicated nonlinear input-output relationship. Mutual entropy analysis is reliable for identifying the influence factors for complex seawater intrusion model.The key factors of seawater intrusion model is identified by mutual entropy analysis.Precipitation rate and groundwater pumping are the key factors for seawater intrusion.The hydraulic conductivity of zone 1 has significant influence on seawater intrusion.