Bimodal atomic force microscopy (AFM) is an important branch of multi-frequency AFM, which can simultaneously obtain the surface morphology and properties of samples. However, the atomic-scale phenomena in the vibration process of bimodal AFM have not been observed due to the absence of atomic-scale model. In this paper, the molecular dynamics (MD) simulations are used to model bimodal AFM. A double springs oscillator model is used to describe the first two vibration mode of the AFM cantilever. By applying dual-frequencies excitation, the dynamics of the model tip and the tip–substrate interactions are observed. The amplitude, phase shift and the average force change of the tip obtained in the simulation were found to be consistent with the continuum simulation results. The effect of different amplitude ratios on the vibration response of the tip is analyzed and validated by experiments. This novel model makes it possible to simulate two vibration modes of cantilever at atomic scale in bimodal AFM.