Harbors are designed to provide the safe loading, unloading and sheltering for the moored vessels. In seasonal weather conditions, semi-enclosed harbors experienced high resonance, which amplifies the surface wave amplitude in the interior of the harbor due to combined effect of wave refraction, diffraction and partial reflection from the solid harbor walls. An accurate description boundary of the harbor is required to analyze the impact of resonant frequency waves over surface ocean wave height. The fluid domain is divided into two regions as bounded and open sea region. The bounded region consists of harbor boundary and interior of the harbor and open sea region consists of ocean area outside the bounded region. Firstly, the mild slope equation (MSE) is derived for both the regions in terms of a potential function using the energy conservation principle. The total wave energy in the bounded region is estimated by using a mathematical model based on Hybrid Finite Element Method (HFEM) is used to formulate the mild slope equation. In HFEM model, the finite element method is coupled with the boundary element method to solve the mild slope equation in both the region. Further, the present HFEM model is validated with existing studies lead by Lee (1971) and Ippen and Goda (1963). The current numerical model is implemented on realistic Pohang New Harbor (PNH), which is situated on the southeast coast of South Korea. The present numerical model can be used as an efficient engineering tool for planning and designing of the artificial industrial harbor and predict the incident wave response under the resonance conditions.