The problem of vibration and noise caused by the propulsion shaft system in modern ships has become increasingly prominent. Floating raft isolation system is an emerging technology used to reduce vibration and noise, which can effectively reduce the transmission of shaft system vibration and noise to the hull, improving the safety and comfort of ship navigation. Based on a small experimental platform for marine propulsion shaft system, this paper constructs a finite element model of the floating raft isolation system and conducts simulation analysis using ANSYS finite element software. The vibration level drop of the system is used as the evaluation index to analyse the isolation performance of the floating raft isolation system under vibration excitation. Finally, the middle raft structure in the floating raft is optimized by opening lightening holes on the rib plates of the raft structure to reduce its mass and achieve the goal of vibration reduction and noise reduction. The results show that the optimized raft structure has better isolation effect, which can effectively solve the vibration isolation problem of the propulsion shaft system and provide reference for the design of the floating raft isolation system.