The measurement of the internal temperature rise of high-frequency magnetic components is of key significance in the design, application, and safety regulation of magnetic components. However, the eddy current loss at the metal end of the thermocouple will bring a large additional temperature rise, which distorts the temperature rise measurement in the part with high frequency magnetic field for the high-frequency magnetic element. Firstly, this paper tests the additional temperature rise of thermocouples with different sizes at different frequencies. Through the analysis of the results, the influencing factors and degree of temperature rise error are clarified, which is helpful to select the appropriate thermocouple according to the working frequency in the actual measurement and evaluate and correct errors. In order to further deduct the unpredictable influence of high-frequency magnetic field environment on thermocouples, this paper proposes to correct the additional temperature rise of thermocouples caused by eddy current loss by using the cooling process curve of magnetic components after power failure and combined with the thermal circuit model of the cooling process. At the same time, the neural network method is proposed to deduce the actual temperature rise of the measured point deducting the additional temperature rise of the thermocouple before the data prediction of the cooling characteristic curve, so as to realize the accurate measurement of the hot spot temperature rise in the magnetic element under the high-frequency magnetic field.