The microstructure of highly porous cellulose nanocrystal (CNC) aerogels is investigated via transmission electron microscope (TEM) tomography. The aerogels were fabricated by first supercritically drying a carboxylated CNC organogel and then coating via atomic layer deposition with a thin conformal layer of Al2O3 to protect the CNCs against prolonged electron beam exposure. A series of images was then acquired, reconstructed, and segmented in order to generate a three-dimensional (3D) model of the aerogel. The model agrees well with theory and macroscopic measurements, indicating that a thin conformal inorganic coating enables TEM tomography as an analysis tool for microstructure characterization of CNC aerogels. The 3D model also reveals that the aerogels consist of randomly orientated CNCs that attach to one another primarily in three ways: end to end contact, “T″ contact, and “X″ contact.