The numerical analysis was used to take modal analysis of multi-tank structure, which aimed to better understand the vibration characteristics of multi-tank structure with liquid, to provide the effect of liquid cases on the vibration frequency of multi-tank structure. The liquid cases with different full rate were chosen by the orthogonal optimization test method. The spring-mass model was lastly introduced to illuminate the frequency shift of multi-cell system. The results show that in the liquid cases with the same full rate, the first frequency of single tank and multi-tank structure all increase at low depth with mini magnitude, the frequencies decrease most with the increase of full rate when the 1st and 3rd tanks are simultaneously filled of liquid. In the liquid cases with different full rate, the first frequency of multi-tank structure is affected by the total liquid, full rate and the arrangement of full rate. The spring-mass modal illuminates that the local frequency which is induced by cell is one key of the abnormal phenomenon of multi-cell system.