In order to study the law of salt transportation in the operation of ship lock and its influence on salinity in freshwater area, we set up a three-dimensional numerical model for k-ε two-phase mixed flow. In the model, control equation groups are dispersed by finite volume method, velocity-pressure coupling by SIMPLEC algorithm, time term by single-order implicit expression, and convection term by second-order upwind scheme, with computing area divided by hexahedral mesh. This model is verified by comparison with prototype experimental results of sea water intrusion into a ship lock, and simulated data are well in agreement with measured data of salinity in lock chamber. The simulation results about the process of seawater intrusion into freshwater zone show that 1) distribution of salinity in upstream waterway can be divided to 3 sections: density current section, transition section and diffusion section, whose salt transporting speed reduces in order; 2) salinity periodically changes at each section and it gradually tends to be at a dynamic balance after ship lock operates for a period; 3) as for a given cycle, saline intrusion quantity is big at early stage of ship lock operation, then, it gradually reduces and tends to be stable. The research results offer scientific reference for the design and operation of ship lock.