In the context of the development of aerospace integration, the near-space aircraft is facing the challenge of autonomous navigation under the satellite denial conditions. Pulsar navigation is a promising solution, and its applicability depends on the transmission characteristics of X-rays in near-space. Firstly, in this paper the interactions between X-rays and charged ions, free electrons and other substances in the ionosphere are analyzed, and the mass attenuation coefficients of reflection, scattering and absorption to X-rays with energy of 1–100 keV are presented. Then, based on the NRLMSIS 2.1 model and IRI-2020 model, a stratified model for X-ray transmission in nearspace is established, and the transmission efficiency and flux acquisition method for 1–30 keV X-rays in 60–100 km are obtained. Finally, the variations in transmission efficiency under the conditions of different seasons, latitudes and days and nights are analyzed, and the distribution characteristics of transmission efficiency are described. Analysis results are shown below. 1) Photoelectric absorption plays a dominant role, while coherent scattering and incoherent scattering have relatively minor influence 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 exceeds 80% when the X-ray energy exceeds 10 keV. 3) The transmission efficiency exhibits distinct annual variation characteristics in the Arctic region and Antarctic region 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 the periodic daily variations with daytime decreasing and nighttime increasing, and the amplitude of diurnal fluctuations being no more than 0.82%. The results indicate that the transmission efficiency peaks in the early morning of the Antarctic winter for 10 keV X-rays at 75 km. Taking Antarctic China Zhongshan Station for example, it can reach up to 93.57%, which means 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 nearspace.