Modal analysis is the basis for studying the torsional vibration characteristics of the generator set shaft system. Current researches mainly focus on modal analysis under conventional shaft system constraints or the characteristic analysis of key parts of the shaft system under certain operating conditions. However, there is insufficient research on the impact of actual operating conditions on the modal characteristics of the shaft system. Taking the shaft system of a 600 MW steam turbine generator set as the research object, firstly, a three-dimensional model of the shaft system is established using the family table parameterization function of Creo modeling software. Then, theoretical analysis and finite element simulation are performed on the conventional natural modes, rotational speed pre-stress modes, thermal pre-stress modes, and modes under the combined effect of rotational speed and thermal pre-stress. The simulation results show that when rotational speed or thermal pre-stress acts separately, the natural frequencies of the shaft system decrease. When both rotational speed and thermal pre-stress act together, the natural frequencies of the shaft system are lower than those under no pre-stress conditions. However, under the premise that the rotational speed is at the nominal operating speed, a phenomenon is observed where the natural frequencies increase gradually with the rise in temperature, compared with the case where only temperature pre-stress is applied. This provides a reference for the design of the shaft system considering actual operating conditions.