The electromagnetic parameters of materials are characterized by complex permittivity and complex permeability. Owing to the nonlinearity of the formulas for solving electromagnetic parameters based on the transmission/reflection method, numerous sources of uncertainties and their correlations, it is extremely complicated to analyze the uncertainty of the measuring results of material electromagnetic parameters using the analytical methods. In this paper, Monte Carlo method is introduced to simplify the analysis and to study the key factors influencing the system uncertainty. The uncertainties of the amplitude and phase of the S parameters measured by the vector network analyzer and the uncertainties introduced by the dimensional tolerance of the waveguide fixture are deduced, and the various uncertainty sources and their probability density functions are analyzed. Taking the measurement of the electromagnetic parameters of PTFE sample at 18GHz to 26.5GHz frequency band as an example, the systematic uncertainty of the measurement is analyzed using the Monte Carlo method, and an uncertainty budget at 22GHz frequency point is given. The influence mechanism of the sample's own electromagnetic parameters on the measurement uncertainty is elucidated. The research results indicate that the Monte Carlo method can effectively analyze the uncertainty of the measuring results of material electromagnetic parameters based on waveguide devices. For the PTFE sample in the example frequency range, the uncertainties of the amplitude and phase of the S parameters are the main factors affecting the uncertainty of electromagnetic parameters measurement results. If the electromagnetic parameters of the tested sample cause the vector network analyzer receiver to receive power within the noise and crosstalk influence area, the uncertainty of the measurement results will increase significantly.