The ship floating raft system adopts the integrated design of large liquid tanks and rafts, which can optimize the arrangement in the cabin and increase the intermediate mass of the system to achieve efficient vibration isolation of equipment. One of the major challenges is that the change of liquid mass in the tank will cause displacement of the raft, which will change the modal characteristics of the system and affect the stability of the vibration isolation system performance. This paper establishes a mechanical analysis model of a floating raft system under time-varying liquid mass conditions. Taking a ship variable mass floating raft system as the research object, the effect of mass change on the characteristics of raft displacement, isolator load distribution, and modal frequency of the vibration isolation system is analyzed. The analysis shows that when the liquid tank goes from full load to no-load state, its mass change accounts for 40% of the total mass of the raft, which will cause a large displacement of the raft and change the low order modal frequency of the system, bringing the risk of equipment safety and vibration isolation performance degradation. Therefore, an adaptive variable load control method is proposed to realize the raft attitude balance and load equalization optimization under the variable mass condition of the floating raft air spring system. The test results show that the proposed control method can automatically adapt to the large mass gradual change from full load to no load of the liquid tank on the raft, and control the displacement of the raft structure from about 10 mm to 1.5 mm, which effectively ensures the stability of the air spring system performance.