Modal performance of a bolted structure is important when considering a precise mechanical product. Joint interface is a critical aspect of a bolted structure, which is difficult to analyze because of its rough profiles. Equivalent material (EM) is used to simplify the joint interface, which reduces the computational cost and modeling difficulty. Using a modified fractal model based on an oblique asperity contact, we calculated the elastic modulus, the shear modulus, the Poisson’s ratio, and the density of EM. The finite element method was applied to discriminate between the resonant frequencies of bolted structures with EM and without EM. The simulation results are compared with the classical frequency response experiment. The errors between experiments and the bolted structures with EM are less than 10%, which are much less than those without EM. It can be concluded that bolted structures with EM are more reliable and reasonable. Furthermore, the effect of EM is more obvious when the joint interface has a small size, roughness, and tightening torque.