For the vibration response analysis of ship hull structure using whole ship model, it is important to consider the influence of liquid such as sea water around the hull, sea water in ballast tanks, crude oil in cargo holds of tanker. And it is known that when tank containing liquid vibrates in horizontally or rotationally, the effective mass of vibration does not coincide with the total mass of contained liquid due to the free surface effect of the liquid. In this paper, the influence of modeling method of liquid in tank for the whole ship vibration analysis has been investigated. First, the characteristics of effective mass of contained liquid when a tank is sinusoidally oscillated horizontally or rotationally respectively are reviewed qualitatively using series expansion method for liquid motion in the tank. Next, the influence of effective mass of liquid in tank on the vibration analysis of hull girder vibration modes has been investigated. Natural frequencies of hull girder vibration modes obtained by using accurate virtual mass method and simplified method for tanks are compared with the measurement results at the sea trial. And the reason of the discrepancy between the results of virtual mass method and simplified one is discussed and investigated quantitatively by using block models of tanks which are extracted from the whole ship model.