To improve the accuracy of calibration results of photoelectric cup-type wind speed sensors, the GUM method and MCM method were used to evaluate the measurement uncertainty of calibration results under the wind speed measurement system. Firstly, the measurement principle and model of photoelectric cup-type wind speed sensor, GUM and MCM are introduced. Then, the uncertainty of the measurement results is evaluated by GUM and MCM, respectively, and the applicability of the GUM method is verified by MCM. Finally, the application of GUM and MCM in the measurement uncertainty evaluation of photoelectric cup-type wind speed sensors is evaluated comprehensively from the aspects of application scope, operability, and accuracy of evaluation results. The results show that: 1) Compared to the GUM (Based on the LPU method), the uncertainty evaluation results of MCM (Based on the LPD method) are more realistic, reliable, and accurate and have higher evaluation efficiency and stronger operability; 2) By comparing and verifying the evaluation results of GUM and MCM, it was found that the absolute deviations dlow and dhigh exceeded the corresponding numerical tolerances, indicating that the GUM method did not pass the applicability verification;3) The uncertainty evaluation results of MCM and adaptive MCM were consistent, and the number of test samples for adaptive MCM (M = 2×104) is much smaller than the number of MCM test samples for a single batch (M = 106). Therefore, when evaluating the measurement uncertainty of the calibration results of the photoelectric cup-type wind speed sensor, it is recommended to use the MCM method. In addition, to reduce the number of randomly selected test samples, the adaptive MCM method can be prioritized.