In the context of integrated space-air development, the near-space aircraft is facing the challenge of autonomous navigation under conditions of satellite denial. Pulsar navigation is a promising solution, and whether it can be applied depends on the transmission characteristics of X-rays in near-space. Firstly, this paper analyzes the interaction between X-rays and charged ions, free electrons and other substances in the ionosphere, and gives the mass attenuation coefficients of reflection, scattering and absorption to X-rays with energy of 1-100 keV. Then, based on the NRLMSIS 2.1 and IRI-2020 models, a stratified model for X-ray transmission in near-space is established, and provides the transmission efficiency and flux acquisition method for 1-30 keV X-rays in 60-100 km. Finally, we analyzes the variations in transmission efficiency under different season, latitude and day-night, and describes the distribution characteristics of transmission efficiency. Analysis indicates that: (1) Photoelectric absorption plays a dominant role, while both coherent and incoherent scattering have relatively minor impacts and the reflection effect is extremely weak and negligible for X-rays applicable to pulsar navigation; (2) The transmission efficiency exhibits a significant positive correlation with X-ray energy and altitude, and it usually surpasses 80% when the X-ray energy exceeds 10 keV; (3) The transmission efficiency exhibits distinct annual variation characteristics in the Arctic and Antarctic regions and subtle semi-annual variation characteristics in the equatorial region. It peaks in the winter hemisphere and reaches a minimum in the summer hemisphere, with the amplitude of its fluctuations in polar regions far exceeding that in the equatorial region. Additionally it also shows periodic daily variations with daytime decreases and nighttime increases, and the amplitude of diurnal fluctuations being no more than 0.82%. The results indicate that the transmission efficiency peaks during the early morning of the Antarctic winter for 10 keV X-rays at 75 km. Taking Antarctic China Zhongshan Station as an example, it can reach up to 93.57%, which represents a 9.61% increase over the summer minimum of 83.96%. This study provides crucial data for supporting the applications of X-ray pulsar navigation in near-space.