In practice, the modeling and analysis of nonlinear rotor-bearing systems are difficult due to the nonlinearity and complexity. In the previous studies, finite element simulation and mathematical modeling methods are mostly adopted to conduct the analysis. However, due to the time-consuming problem in finite element simulation and the lack of sufficient prior knowledge in mathematical modeling, the traditional method is difficult to establish the representation model. In order to overcome this issue, in this study, a data-driven model referred to as the NARX (Nonlinear Auto-Regressive with exogenous inputs) model is introduced to conduct the modeling and analysis of the rotor-bearing system. The identification of the NARX model requires random excitation as the system input, while the input signal of the rotor system is harmonics. Therefore, a time-domain frequency sweep modeling method is proposed in this paper by introducing the rotating speed into the coefficients function expression of the NARX model, the system output can be predicted according to the given speed. Moreover, the representation model of the rotor-bearing system obtained by using the proposed method is validated under different rotating speeds, the results show the applicability of the proposed modeling approach. Finally, an experimental case of the rotor-bearing test rig is demonstrated to show the application in practice. Both the numerical and experimental studies illustrate the applicability of the proposed modeling method, which provides a reliable model for dynamic analysis and fault diagnosis of the rotor-bearing system.