The invention relates to a method for calculating a natural frequency of a honeycomb sandwich plate, which comprises the following steps of: by measuring bending rigidities D11, D12, D22 and D66 of the sandwich plate, shear moduli Gxz and Gyz of a core layer in x-z and y-z planes, a length a and a width b of the sandwich plate, a panel thickness t, a core layer thickness h and a panel density rho<f> and a core layer density rho<c> of the sandwich plate, calculating to obtain shear stiffnesses Cxz and Cyz of the core layer and an equivalent face density rho; and substituting the measured data into a formula to calculate so as to solve the natural frequency omega<m> of an mth order of the sandwich plate. According to the invention, a bending vibration equation system form and the process of solving the natural frequency of the sandwich plate are simplified, the influence of the transverse shear deformation of the core layer and the integral orthogonal anisotropy of the sandwich plate on the mechanical property of the sandwich plate is also considered, the calculating process of the natural frequency is simplified, the calculating efficiency is improved, the calculating difficulty is reduced and the calculating accuracy of the natural frequency is improved.