Taking ship vibration isolation systems as the research subject, the particle damper was applied to ship vibration isolation systems to study its vibration reduction performance. The energy dissipation mechanism of particle dampers is analyzed, and an energy dissipation calculation model is derived. The combined method of simulation and experimentation is employed to study the influence of parameters such as particle material, filling rate, particle diameter, and collision coefficient of restitution on the vibration reduction performance of particle dampers. The impact laws of these parameters are summarized, demonstrating that particle dampers can produce excellent vibration reduction performance when applied in ship vibration isolation systems, and reasonable parameter recommendations are provided. Response surface method (RSM) is used to fit an accurate energy dissipation prediction model and calculate the optimal performance parameters. This paper serves as a valuable reference for the parameter design, optimization, and practical engineering applications of particle dampers.