The motion tracks of high energy accelerated electron in AlxGa1-xN crystal film material are simulated by Monte Carlo method, The relationships between accelerated voltages and the depths which kV voltages accelerated electron can reach are studied. The experimental thickness of crystal film epitaxial layer is measured by ultraviolet visible light transmittance spectra method. The aluminium composition of crystal film epitaxial layer is determined by electron probe microanalysis/wavelength dispersive spectrometer (EPMA/WDS) method, with suitable experimental parameters of accelerated voltage and current and beam diameter from theoretical simulation. The experiment is carried out between two EPMA laboratories, six samples by each laboratory. The source of measurement uncertainty is analyzed including measurement reproducibility and X-ray intensity and physical parameter etc.. The experimental results show that the measurement uncertainty of EPMA/WDS for the determination of aluminium composition (x=0.8) is 2.7×10-2, the coverage factor k is 2.