The influence of existing prestress on structure dynamic response and acoustic radiation were investigated. Based on Flügge’s cylindrical shell equations, the strain-displacement equation with prestress in local areas was discussed, and the structural-acoustic mathematical formulation for cylindrical shell with prestress in local areas was propored by using the variational principle. By using finite element method (FEM) and boundary element method (BEM), the numerical analysis of structural-acoustic radiation for shell structure was presented, and the influence comparison of prestress on acoustic radiation power and acoustic radiation directivity was conducted. The results show that with the existing of prestress in local areas leads to a change of local areas stiffness matrix, and the overall stiffness matrix of cylindrical shell is altered. The prestress has a significant impact on dynamic characteristics of cylindrical shell structure.