Turbomachinery such as turbines, pumps and compressors, which are installed in transportation systems, including aircrafts, ships, and space vehicles, etc., often perform crucial missions and are exposed to potential dangerous impact environments such as base-transferred shock forces. To protect turbomachinery from excessive shock forces, it may be needed to accurately analyze transient responses of their rotors, considering the dynamics of mount designs to be applied. In this study a generalized FE transient response analysis model, introducing relative displacements, is proposed to accurately predict transient responses of a flexible rotor-bearing system with mount systems to base-transferred shock forces. In the transient analyses the state-space Newmark method of a direct time integration scheme is utilized, which is based on the average velocity concept. Results show that for the identical mount systems considered, the proposed FE-based detailed flexible rotor model yields more reduced transient vibration responses to the same shocks than a conventional simple model, obtained by treating a rotor as concentrated lumped mass, equivalent spring and a damper or Jeffcott rotor model. Hence, in order to design a rotor-bearing system with a more compact light-weighted mount system, preparing against any potential excessive shock, the proposed FE transient response analysis model herein is recommended.