Bevel gears are essential in aviation transmission systems. With the rising demand for higher gear power density, vibration issues have become increasingly significant. Traditionally, gears are treated as rigid bodies in dynamic analyses, but this method may not suit high-power density bevel gears with thin-walled structures. This paper develops a dynamic model that incorporates the flexibility of the bevel gears rotor system. Using three-dimensional hexahedral elements offers a precise representation of the gear’s web, teeth, and shaft, maintaining structural integrity. The model is simplified through the component mode synthesis method, enhancing computational efficiency without sacrificing accuracy. The system-level modal frequencies and vibration modes of the bevel gear shaft are compared with ABAQUS results to validate the model. The vibration mode shapes of critical modal frequencies, identified through modal strain energy analysis, were cross-validated with vibration displacement cloud maps at resonance speeds calculated using the Newmark-β method. This analysis indicates that high-power density bevel gears are more susceptible to nodal diameter type vibrations.