Based on MIKE3 FW model，we establish the three-dimensional salinity mathematical model covering eight entrances to study the problem of saltwater intrusion.Triangles was mainly adoptted，and quadrilateral grid was used to refine the straight channel.The validation is better，and the three-dimensional hydrodynamic and salinity distribution characteristics in Pearl river mouth area are reflectted.The three-dimensional hydrodynamic and salinity characteristics in Modaomen sea area are mainly analyzed and the influence of saltwater intrusion about the Modaomen waterway regulation project is studied.The results show that the salinity value and saltwater intrusion distance are increased by waterway regulation engineering.But the influence is small，and it is not the main reason for the saltwater intrusion in recent years.