Several damping materials have been employed to reduce the vibration of marine structures. In this paper, a new method of identifying system matrices for non-proportional damping structures using modal parameters is proposed. This method has two advantages. First, the mass and stiffness matrices do not need to be calculated using the FEM, so errors due to the inaccuracy of these matrices can be reduced. Second, various indirect methods can be used to identify modal parameters such as natural frequencies, modal damping ratios and mode shapes. Three case studies of lumped mass systems with non-proportional damping are carried out to verify the performance of the proposed method in this study.