In this study, the performance evaluation of a conventional wave resonator at the entrance of a port or a pier against secondary undulation has been performed using 2D hydrodynamic modeling within port. A wave resonator has been designed for the attenuation of the secondary undulation induced by the long-periodic waves. The controlled performance of the wave resonator has been numerically investigated for CGWAVE MODULE of finite-element model of SMS (Surface water Modeling System) based on the elliptic mild-slope wave equation. SMS was verified though the comparisons with analytical solution performed by Ippen and Goda (1963). Also, It was confirmed that a wave resonator of a rectangular model harbor is effective enough to control the secondary undulation when it compares variation of water level with the case of no resonance system. From the above results, amplification phenomenon induced by long-period waves transferred from 1900 sec to 2100 sec when it applied a wave resonator in Busan Gamcheon Port which is a deep-sea. And it was confirmed that a wave resonator of Pohang New Port attenuates largely long-period waves which are within the range of 300 sec induced by long-period motion of the moored ship.