Spiral bevel gear is widely used in various mechanical transmission systems, such as tractor transmission system. Because it is mainly used in the heavy-load conditions, it would most likely resonate within the rated speed, resulting in tooth fatigue damage. In this paper, based on the principle of meshing and gear tooth machining, the spherically involute tooth profile equation of spiral bevel gear is deduced and the precise modeling method based on the CATIA is studied. The natural frequency and modal shape under free vibration are obtained by the finite element method (FEM), the influence of web thickness and web hole on the natural frequency of driven gear plate is analyzed as well. In addition, the experimental modal of bevel gear pair is carried out based on a multiple-reference impact test, Modal Assurance Criterion (MAC) is calculated, the three-dimensional modeling accuracy and the finite element analysis reliability are verified. The results show that the error between the measured frequency of bevel gear pair and the calculated frequency of the finite element simulation are both within 5%, and the MAC is above 0.8. The fourth-order natural frequency is the most sensitive to the web thickness, the second-order natural frequency is the most sensitive to the web hole.