The invention provides a method for checking the fatigue strength of a connecting flange of a fan tower drum. Firstly, a finite element model of the connecting flange of the fan tower drum is established. Then the fatigue limit loads with opposite directions are applied to the center of the upper flange and the lower flange respectively in the finite element model of the connecting flange of the fan tower drum, and the nonlinear solution of the finite element model under the fatigue limit condition is carried out, and the relationship between the connecting flange load and the shear stress onthe surface of the connecting flange is obtained. Combined with the fatigue time series load spectrum of the flange position, the fatigue damage value of the connecting flange is calculated. As the technical proposal provided by the invention directly calculates the fatigue strength of the connecting flange, and when the fatigue limit load is applied, the fatigue strength of the connecting flangeof the fan tower drum can be accurately calculated because the fatigue limit load is the same as the actual stress causing the fatigue of the connecting flange.