The miniature transmission X-ray tube is widely used in energy dispersive X-ray Fluorescence Analysis (EDXRFA). The miniature transmission X-ray tube with a small, low power consumption, X-ray emission efficiency that can be made the excitation source of handheld X-ray energy dispersive fluorescence analyzer. Beryllium (Be) is the most commonly used X-ray window material. But beryllium is expensive and toxic. At the same time set filtering window by aluminum (Al) to reducing low-energy scattering rays. This paper be adopted Al for exit window material of miniature transmission X-ray tube, achieve high-energy rays transmission and low-energy scattered radiation shielding, at the same time reduce production cost and difficulty. The present paper simulate the X-ray tube output spectrum of silver (Ag) target and aluminum window with different thickness by MCNP5. We consider the X-ray of low energy part is completely shielded when aluminum windows thickness is greater than 1.5 mm. We can conclude that 2 μm and 0.8 mm are the best combination of target thickness and aluminum windows through comparative analysis of existing research results. Then we can get flux of high energy part is big and low energy part is small when the target is 2 μm thick Ag and the window is 0.8 mm thick Al.