We present new measurements of the vertical density profile of the Earth’s atmosphere at altitudes between 70 and 200\,km, based on Earth occultations of the Crab Nebula observed with the X-ray Imaging Spectrometer onboard Suzaku and the Hard X-ray Imager onboard Hitomi. X-ray spectral variation due to the atmospheric absorption is used to derive tangential column densities of the absorbing species, i.e., N and O including atoms and molecules, along the line of sight. The tangential column densities are then inverted to obtain the atmospheric number density. The data from 219 occultation scans at low latitudes in both hemispheres from September 15, 2005 to March 26, 2016 are analyzed to generate a single, highly-averaged (in both space and time) vertical density profile. The density profile is in good agreement with the NRLMSISE-00 model, except for the altitude range of 70–110\,km, where the measured density is $\sim$50\% smaller than the model. Such a deviation is consistent with the recent measurement with the SABER aboard the TIMED satellite (Cheng et al. 2020). Given that the NRLMSISE-00 model was constructed some time ago, the density decline could be due to the radiative cooling/contracting of the upper atmosphere as a result of greenhouse warming in the troposphere. However, we cannot rule out a possibility that the NRL model is simply imperfect in this region. We also present future prospects for the upcoming Japan-US X-ray astronomy satellite, XRISM, which will allow us to measure atmospheric composition with unprecedented spectral resolution of $\Delta E \sim 5$\,eV in 0.3–12\,keV.