In this paper, the symplectic perturbation series methodology of the non-conservative linear Hamiltonian system is presented for the structural dynamic response with damping. Firstly, the linear Hamiltonian system is briefly introduced and its conservation law is proved based on the properties of the exterior products. Then the symplectic perturbation series methodology is proposed to deal with the non-conservative linear Hamiltonian system and its conservation law is further proved. The structural dynamic response problem with eternal load and damping is transformed as the non-conservative linear Hamiltonian system and the symplectic difference schemes for the non-conservative linear Hamiltonian system are established. The applicability and validity of the proposed method are demonstrated by three engineering examples. The results demonstrate that the presented methodology is better than the traditional Runge–Kutta algorithm in the prediction of long-time structural dynamic response under the same time step.