The dynamic response of rotating systems supported by hydrodynamic bearings considering the journal deformation-induced misalignment has been investigated in recent years. However, most of the previous work studied misaligned angles as fixed configurations, ignoring the variation of misalignment due to the time-varying journal deformation. In this study, a numerical method is proposed to predict the dynamic response of a rotor-bearing system considering time-dependent misalignment. As journal deformation is recognized as a significant factor leading to misalignment, a flexible rotor is considered to determine the misalignment state. The finite element method is employed to calculate the dynamic deformation of the rotor and, hereby, the misaligned angles and film thickness. Subsequently, the pressure distributions of the oil film are calculated using the finite difference method to update the bearing force. The transient lubrication performance and the vibration response of the rotor are discussed based on the numerical computation. In particular, the difference in the oil whip phenomenon is compared between the aligned and misaligned conditions. The results show that the journal orientation varies with time considering the journal deflection. The discussion about the oil whip shows that the misalignment has a significant impact on the stability of the system. In addition, the transient lubrication properties are considerably influenced by the rotation speed and external loading since they affect the magnitude of the resonance vibration and the oil whip.