At the moment of electric locomotive passing the neutral-section, the voltage and current of traction network may have low-frequency oscillation (LFO), which will seriously affect the safe operation of the railway. Aiming at eliminating LFO, a modeling method of vehicle-grid coupling system based on flux-current theory is presented in this paper. In the model of electric locomotive, the transient current control strategy and magnetic saturation of on-board transformer are considered, and the equivalent model of excitation inductance of on-board transformer is established based on the flux-current theory. Using this model, based on the Middlebrook impedance ratio criterion, the stability region of vehicle-grid coupling system is analyzed under the influence of average saturation of on-board transformer and control parameters of electric locomotive. Simulation results and analysis are established to evaluate and verify the proposed modeling method of LFO. This work has the benefits of defining the opening and closing phase angle region of system stability as well as providing guidance to adaptively modify the control parameters to suppress the LFO.