In this paper, a winding loss calculation method used in the field of converter transformer is introduced into the field of high frequency transformer for the first time, and the influence of winding structure on the calculation accuracy of the method is considered for the first time. Taking the results of finite element simulation as the reference value, the calculation results of this method are compared with those of the formula method. The feasibility of using this method to calculate the winding loss of high frequency transformer is verified. Firstly, the winding loss of rectangular wire commonly used in small capacity high frequency transformer is analyzed. Based on the finite element simulation results, the calculation accuracy of the new method and the formula calculation method is compared to prove the feasibility of the new method. Then, using the same method, the accuracy of the new method and the formula method in calculating the winding loss of the round wire also used in the small-capacity high-frequency transformer is compared. The maximum number of continuous winding layers is changed, and the results of different layers are calculated. Finally, the cross transposition winding structure is also calculated, which proves that the new method is not only suitable for different shapes of wires, but also suitable for different winding structures. The results show that the new method has good calculation accuracy and good applicability, and can obtain more accurate calculation results of winding loss of high-frequency transformers with different shapes of windings.