In order to insure the water safety of water source affected by saltwater intrusion in the downstream of Minjiang River,the paper established a two-dimensional numerical model based on environmental fluid dynamics code (EFDC).It calibrated the parameters of the model by using synchronous data in December 2013 and simulated the distance of salinity intrusion and the impact on water source land under the condition of different flows. Results indicate that the range of salinity intrusion is negatively correlated with the discharged; the increase of saltwater intrusion distance will extend the unsuitable water intake time of water source in the downstream of Minjiang River. In order to mitigate the impact of saltwater intrusion on water source, the paper recommended that it is necessary to optimize the operation ways of Shuikou reservoir and increase discharged.