When the finite element method is employed to calculate the mechanical behaviors of a corrugated sandwich panel structure, the numerical model occupies a large amount of computational resources, which usually causes the problem of long-time solution. In order to reduce the scale of the finite element model and to quickly perform the dynamic analysis of such type structures, in this paper the middle corrugated sandwich layer is simplified into a homogeneous orthotropic plate. Then, based on the third-order shear deformation theory, the equivalent stiffness matrix of the corresponding plate element is formulated from adequate performance analyses of the corrugated sandwich plate. Afterwards, the natural frequencies of two corrugated sandwich plate structures in the cantilevered and free states are obtained respectively through the test and numerical calculation. By comparing with the experimental results, the effectiveness of the equivalent finite element model is verified. It turns out that the obtained results are much better than those based on the first-order shear deformation model. Moreover, the method proposed in this work can be utilized efficiently for modal parameter computations of the corrugated sandwich plates with the high accuracy.