The mathematical model is constructed based on 3-D Boundary Element Method (BEM) with the consideration of diffraction, reflection and refraction of multidirectional incident waves utilizing the Laplace equation in a complex geometry harbors. The geometry of the harbor is divided into bounded and open sea region. The partial reflection boundary with variable bathymetry is also considered to analyze the wave spectrum. A Mitsuyasu’s wave spectrum is applied to estimate the wave spectrum with multidirectional incident waves. The current numerical approach is practically applied on realistic Pohang New Harbor (PNH), Pohang South Korea. The validation of numerical scheme is done by comparison of measurement data with simulation results at different port stations. Therefore, the current numerical approach is provide the efficient numerical tool to foster the prediction of wave-induced oscillation in a harbor with irregular geometry.