The motion of the moored ship in the harbor is a classical hydrodynamics problem that still faces many challenges in naval operations, such as cargo transfer and ship pairings between a big transport ship and some small ships. A mathematical model is presented based on the Laplace equation utilizing the porous breakwater to investigate the moored ship motion in a partially absorbing/reflecting harbor. The motion of the moored ship is described with the hydrodynamic forces along the rotational motion (roll, pitch, and yaw) and translational motion (surge, sway, and heave). The efficiency of the numerical method is verified by comparing it with the analytical study of Yu and Chwang (1994) for the porous breakwater, and the moored ship motion is compared with the theoretical and experimental data obtained by Yoo (1998) and Takagi et al. (1993). Further, the current numerical scheme is implemented on the realistic Visakhapatnam Fishing port, India, in order to analyze the hydrodynamic forces on moored ship motion under resonance conditions. The model incorporates some essential strategies such as adding a porous breakwater and utilizing the wave absorber to reduce the port’s resonance. It has been observed that these tactics have a significant impact on the resonance inside the port for safe maritime navigation. Therefore, the current numerical model provides an efficient tool to reduce the resonance within the arbitrarily shaped ports for secure anchoring.