This study proposes a tool for analyzing the tsunami outbreaks in coastal cities based on a 3D particle method of Smoothed Particle Hydrodynamics (SPH). Firstly, we obtain the 3D location information (SHP) and Digital Elevation Model (DEM) through the Geographic Information System (GIS), thus display the topography, altitude, and the outside appearance of the buildings. Then, the STL data defined by the surface profile are converted to particle data. Finally, the incompressible condition in the SPH method is alleviated, and the boundary problem is solved by virtual marking. The 3D simulations show that the tsunami particles do not penetrate into the buildings, and there is no gap between the buildings and the ground, which verifies the good results of the proposed method.