According to the requirement from the helicopter rotor system dynamic modeling method based on the flexible multibody system dynamics method, a time-domain embedded multi-layer elastomeric damper model based on internal variable theory was developed in consideration of the structural characteristics of the embedded multi-layer elastomeric damper. By using the multi-layer internal variable field, the model is more capable to calculate the dynamic characteristic of the damper over a wide strain amplitude and excitation frequency range and under dual frequency excitation condition. The influence of the metal shims of embedded multi-layer elastomeric damper was considered in modeling process, and the influence of the temperature rise during the damper operation on elastomeric material was considered by temperature shift function, improving the accuracy of damper. The calculational results and the experimental data were compared to verify the effectiveness of damper model under different strain amplitudes, excitation frequencies and dual frequency excitation conditions. This work provides an embedded multi-layer elastomeric damper model for calculating and analysis of helicopter rotor system aeroelastic stability.