The nanoparticle supercrystals (NPSCs) have been of great interest for their collective emergent properties. While various NPSCs have been successfully fabricated using intermolecular forces, the limited structural stability of NPSCs due to the weak nature of the intermolecular forces often limits their practical applications. Herein, we report a new method to fabricate highly stable three-dimensional NPSCs by using aldol reaction, a model covalent bond-forming reaction, in conjunction with slow solvent evaporation. Gold nanoparticles functionalized with formyl poly-ethylene glycol thiol are linked to each other by carbon-carbon covalent bonds formed by the aldol reaction as the particle dispersion in aqueous NaOH solution is slowly evaporated, resulting in highly faceted three-dimensional NPSCs. The as-synthesized NPSCs show excellent structural stability in solvents of different polarities as well as the dried condition and at temperature up to 160 °C, which is far superior to NPSCs stabilized by intermolecular forces such as hydrogen bonding and van der Waals interactions. A new covalent bonding approach opens up new opportunities in the synthesis of NPSCs and their applications.