For non-classically damped systems, it is easy to construct a damping matrix based on a hysteretic damping model. However, the damped natural frequency is non-physical, and the frequency response function is non-causal. These two drawbacks can be overcome by the hysteretic damping model with frequency-dependent loss factors. In this paper, a complex mode superposition method for non-classically damped systems based on the hysteretic damping model with frequency-dependent loss factors is proposed. Frequency-dependent loss factors of the natural frequencies are considered in the transient vibration response, while frequency-dependent loss factors of the external excitation frequencies are considered in the steady state vibration response. By decoupling complex modes in state space and physical space, non-proportional damping characteristics of hybrid structures can be effectively considered. Therefore, the proposed method can be used to calculate the time-domain dynamic responses of hybrid structures, whose loss factors are sensitive to frequency variation and have strong non-proportional damping characteristics. The time-domain dynamic responses of numerical examples are compared based on different mode superposition methods. Shaking table tests are performed on cantilever plates with different damping characteristics. The numerical and test results validate the proposed method. Moreover, the proposed method has a wide range of applications.