Vibration analysis is crucial for studying rotor dynamics. The gas turbine rotor system is subjected to complex alternating loads during navigation, resulting in vibrations transmitted to the bearings that alter the system’s dynamic characteristics. Based on the similarity law of the wave resistance test, a hull model was established. Beam sea and head sea tests were conducted in the towing pool to measure the acceleration response at the key positions. A finite element model of the turbine rotor system was established, and the test data were imported into the model after wavelet noise reduction and resampling to calculate the vibration response at the front and rear bearing points. The vibration responses transmitted to different locations and directions caused by beam sea and head sea conditions were analyzed. A comparison and analysis were conducted on the acceleration responses in various locations and directions under beam sea or head sea conditions. The equivalent von Mises stress distribution of the gas turbine rotor system under beam sea and head sea loads was obtained. The vibration transfer model was verified for accuracy and can be used to quickly analyze the vibration response of bearings under wave load transfer. This study provides a theoretical basis and reference for enhancing the stability of the gas turbine rotor system.