The invention discloses a calculation method of natural frequencies of a transformer winding. A two-dimensional axisymmetric model of the transformer winding is built in an ANSYS; equivalent densities and equivalent elastic moduli of a transformer winding structure are calculated, and material attribute parameters are defined and assigned in the ANSYS. A grid structure is divided, a grid shape is controlled, and occurrence of distortion is avoided. Winding displacement constraint conditions are set, and full displacement constraints are respectively exerted on the upper boundary of a pressure plate and the lower boundary of a support plate. Modal analysis is carried out on the model, and a calculation result is output. The equivalent elastic moduli of a cushion block layer, an end coil and an end insulation are modified, action effects of different pre-tightening forces are enabled to be equivalent, and the various order natural frequencies of the winding are calculated. The method has the advantage that quickly and equivalently calculating the various-order natural frequencies under the different pre-tightening forces can be realized.