Bubble pulsation load caused by underwater explosion could induce whipping response of slender structures, and even threaten the overall strength. As the classic structure form of submarine, research on the whipping response of cylindrical shell structure is very significant. In this paper, Morrison relative velocity model and hull beam model are combined together to establish the numerical engineering model of whipping response of cylindrical shell structure and validated by comparing with experimental results. Then, time-domain and frequency-domain characteristics of whipping response of a cylindrical shell structure are analyzed to obtain the effect of various case parameters, such as charge depth, axial bias, distance and so on, which is aiming to offer reference for the design and research of submarine shock resistance.