Wave based method (WBM) is presented to analyze the free and forced vibration of cylindrical shells with discontinuity in thickness. The hull is first divided into multiple segments according to the locations of thickness discontinuity and/or driving points, and then the Flügge theory is adopted to describe the motion of cylindrical segments. The dynamic field variables in each segment are expressed as wave function expansions, which accurately satisfy the equations of motion and can be used to analyze arbitrary boundary conditions, e.g., classical or elastic boundary conditions. Finally, the boundary conditions and interface continuity conditions between adjacent segments are used to assemble the final governing equation to obtain the free and forced vibration results. By comparing with the results existing in open literate and calculated by finite element method (FEM), the present method WBM is verified. Furthermore, the influences of the boundary conditions and the locations of thickness discontinuity on the beam mode frequency and fundamental frequency are discussed. The effects of the direction of external force, location of external point force, and the structural damping on the forced vibration are also analyzed.