Applying Monte Carlo method, the present paper simulates the emitted X-ray spectrum of miniature X-ray tube with thirteen thickness of beryllium window in the range from 50 to 500 μm. By analyzing the characteristic of the spectrums, the reasonable choice of thickness of beryllium window relies on the application and for the beryllium window it is not the thinner the better. Taking in-situ EDXRF as an example, though the emission X-ray intensity is higher as the thickness of the beryllium window becomes thinner, the proportion of useless low-energy X-ray (<5 keV) intensity to all energy X-ray intensity also is higher (>20%). The accuracy of in-situ EDXRF will be reduced when the high-throughput low-energy X-ray enters the detector. Therefore, this paper puts forward several parameters as judgment index for beryllium window thickness, which is described as follows: ①The intensity ratios of the K-series X-ray to middle-energy (5～25 keV) bremsstrahlung and middle-high-energy (5～50 keV) bremsstrahlung (F1 and F3); ②The intensity ratios of useless low-energy X-ray (<5 keV) to middle-energy (5～25 keV) X-ray and middle-high-energy (5～50 keV) X-ray (F2 and F4), it can reflect the relative intensity of useless low-energy X-ray. The simulation results demonstrate that with the increase in the beryllium window thickness, the value of F1 (F3) improves slowly, and the value of F2 (F4) decreases rapidly. In addition to the judgment index discussed above, and considering the X-ray shielded by beryllium window, the beryllium window of miniature X-ray tube can be determined. Based on simulation analysis, the thickness of around 250μm is appropriate to miniature X-ray tube applied in the in-situ EDXRF. Comparing the emitted spectrum with 50 μm-thick beryllium window, 71.66% of low-energy X-rays are shielded, only 21.31% of X-rays with energy from 5 to 50 keV is shielded, the intensity ratio of low-energy X-ray to total energy X-ray is less than 10%, and the intensity proportion of K-series X-ray to middle-high energy X-ray maintains a high level. In other words, when the mobile X-ray source with 250 μm beryllium window is used in the in-situ EDXRF, proportion of effective signal is higher, and effect of energy resolution of the detection is least; Moreover, the relative intensity of the excitation spectral scattering background, which is obtained by detection for specimen excitation analysis, will remain at low level, thus to ensure the precision of the result of element analysis. For the beryllium window in the application of radiation therapy, the thicker the better. At this time, low-energy X-ray flux maintains a high level, and it can ensure that radiation dose is concentrated on treatment tissue.