Estimation of wave height and period is in great importance for design of port facility. The harbortranquility is determined according to wave height distribution and occurrence probability in the target berth areas. The crown height of breakwater and sea wall is designed as those facilities protect the inner harbors and water-front areas from the acting waves. The wave transformation model with high accuracy is necessary to keep the harbor safe and effective. In the paper, the practical computation system for port wave is introduced. The energy balance equation model and Bussinesq equation model for wave is employed for estimation of wave transformation in shallow water and very shallow water area respectively. The data base including water depth contours and berth arrangements in the ports is attached with the computation system as the bathymetry data for simulation is completed in short duration.