Abstract The support stiffness and positions of the bearings can greatly affect the vibrations of flexible rotor systems. However, most previous works only focused on the effect of the support stiffness of the bearings on the critical speeds of the rigid rotor systems or modal characteristics including natural frequencies and mode shapes, which missed the combine effects of the support stiffness and positions of the bearings. To overcome this issue, an analytical dynamic model of a flexible rotor system based on the finite element (FE) method is proposed. The model considers the support stiffness of the bearings and rotational inertia of the rotor system. The frequency equation of the rotor system is established for solving the critical speeds. The critical speeds and modal deformations of the system from the presented model and the numerical model based on a commercial software are compared to verify the effectiveness of the proposed FE model. The effects of the support stiffness and positions of the bearings on the critical speeds of the flexible rotor system are analyzed. The results show that the critical speeds are positively correlated with the support stiffness. The critical speeds of the flexible rotor system are also greatly affected by the support positions of the bearing. This study can provide some guidance for the optimization design method of the support stiffness and positions of the bearings in the flexible rotor systems.