In view of the periodic and unsteady aerodynamic loads of pulse detonation turbine engine(PDTE), finite element method was used to establish a dynamic characteristics calculation model for rotor system of PDTE. On the basis of verifying the accuracy of the calculation model, the effects of periodic and unsteady axial force and torque on the dynamics characteristics of rotor system were studied. The results show that compared with traditional gas turbine engine, the rotor system of PDTE has bending vibration, axial vibration and torsional vibration at the same time. Aerodynamic loads of pulse detonation combustor change bending stiffness of rotor system, but it has little effect on bending vibration in case of reasonable design. Periodic and unsteady axial force causes axial vibration of rotor system, and the axial vibration characteristics are mainly affected by the responses at zero frequency and the first order axial resonance frequency. When PDTE is in service state, the axial reaction force of ball bearing changes direction continuously, which should be considered in the design of ball bearings. Periodic and unsteady torque causes torsional vibration of rotor system, and the first order torsional resonance frequency component is dominant in torsional vibration response.