Based on the complex dynamic characteristics of new shell structure, a 3-D nonlinear finite element model of interaction between large cylinder structure, soil and wave is established. The non-linear contact characteristics between shell structure and soil are simulated by setting contact element of zero thickness. The non-linear constitutive model of soil is used to simulate dynamic response analysis of the structure under the dynamic loads on waves. The distribution of stress in x- and y-directions, the changing law of stress with wave and buried depth are obtained. Finally the stress distribution function and reasonable size of cylinder structure are given.