The invention discloses a method for estimating the harmonic loss of a transformer, and belongs to the technical field of electric system energy saving. The method comprises the steps that the iron core loss of the transformer under fundamental waves is analyzed and calculated; the winding loss of the transformer under the fundamental waves is analyzed and calculated; two parameters needed in estimation are calculated according to the measured data of the harmonic loss of the transformer; finally, the harmonic loss of the transformer is estimated. According to the method for estimating the harmonic loss of the transformer, the harmonic loss of the transformer can be estimated easily and fast according to the measured data, certain rationality and accuracy are achieved, and the method can be applied to energy saving and loss reduction work.