This paper provides a time transient method for solving coupled lateral and torsional analysis of a flexible rotor–bearing system including gyroscopic effects, nonlinear short journal bearings, nonlinear short squeeze film dampers (SFDs), and external nonlinear forces/torques. The rotor is modeled as linear, and the supporting components, including bearings and dampers, are modeled as nonlinear. An implicit Runge–Kutta method is developed to solve the nonlinear equations of motion with nonconstant operating speed since the unbalance force and the gyroscopic effect are related to both the rotational speed and the acceleration. The developed method is compared with a previous torsional analysis first to verify the nonlinear transient solver. Then the coupled lateral and torsional analysis of an example flexible three-disk rotor, perhaps representing a compressor, with nonlinear bearings and nonlinear dampers driven by a synchronous motor is approached. The acceleration effects on lateral and torsional amplitudes of vibration are presented in the analysis. The developed method can be used to study the rotor motion with nonconstant rotational speed such as during startup, shutdown, going through critical speeds, blade loss force, or other sudden loading.