In this work, cellulose nanocrystal (CNC) was prepared from microcrystalline cellulose (MCC) by acid hydrolysis method. The N-(2-aminoethyl)(3-aminopropyl) methyldimethoxysilane (AEAPMDS)-CNC aerogel was successfully fabricated either by freeze-drying or supercritical CO2 drying of spherical CNC hydrogels into which the amine group has been successfully introduced via C–O–Si bonds between CNC and AEAPMDS. The impact of various parameters (time, temperature, AEAPMDS amount, solid-to-liquid ratio) on the properties of the as-prepared materials is systematically explored, revealing the optimum reaction conditions (100 °C, 16 h, solid-to-liquid ratio of 1:10). The as-prepared spherical nanocellulose aerogels were characterized with respect to textural, structural, thermal and morphological characteristics by various methods (BET, XRD, SEM, TGA, FTIR, and NMR). They exhibited a nano-porous network structure of mesopores possessing a high surface area (262 m2/g) in the case of supercritical CO2 drying, whereas a honeycomb structure comprising squares, polygons and circles with a surface area of 120.4 m2/g was obtained by freeze-drying. The as-synthesized AEAPMDS-CNC aerogels could be potentially applied to capture CO2 via covalent bonding.