While underwater launched vehicle crossing water free surface, time-varying Fluid Structure Interaction effect is formed due to the interaction between the vehicle and surrounding water and the decrease of wet surface. As a result, the variety of structure dynamic property occurs. Moreover, Compartment structure is widely adopted in underwater lunched vehicle. The joint part between two compartments causes nonlinear contact problem, which effects structure dynamic property. Considering the above factors, the vehicle is simplified into a Timoshenko beam, and mode analysis and transient analysis are conducted. The different effect regularity of the time-varying Fluid Structure Interaction and the nonlinear stiffness at the joint part on the structure natural frequency and dynamic response has been obtained. Besides, the effect of joint structure, external load and water exit velocity on structure dynamic response is analyzed.