Extreme wave oscillation inside coastal regions plays an important role for the harbors or ports directly connected with open Ocean. High amplitude waves coming from the open Ocean destroy the boundary of the ports and moored ships. In seasonal weather condition, when wave oscillation is high it makes the loading and unloading task of moored ship difficult. So, it is required to develop a mathematical model with resonance conditions on moored ship motions. In the mathematical formulation, the domain of fluidis divided into three subdomains namely bounded (subdomains bounded by quays and walls of the port), unbounded (open Ocean) and ship region. A 3-D boundary element approach is employed the Laplace equation inside the bounded region (port) while a 2-D boundary element method is used for open Ocean using Helmholtz equation. The present numerical model is validated with the previous published studies. The moored ship motions (surge, roll, sway, pitch, heave, and yaw) are analyzed under the extreme weather conditions in real Paradip harbor. The safe locations inside the Paradip harbor can be identified for the ship mooringbased on simulation outcomes.