Ordered assemblies of inorganic nanocrystals coated with organic linkers present interesting scientific challenges in hard and soft matter physics. We demonstrate that a nanocrystal superlattice under compression serves as a nanoscopic pressure cell to enable studies of molecular linkers under uniaxial compression. We developed a method to uniaxially compress the bifunctional organic linker by attaching both ends of aliphatic chains to neighboring PbS nanocrystals in a superlattice. Pressurizing the nanocrystal superlattice in a diamond anvil cell thus results in compression of the molecular linkers along their chain direction. Small-angle and wide-angle X-ray scattering during the compression provide insights into the structure of the superlattice and nanocrystal cores under compression, respectively. We compare density functional theory calculations of the molecular linkers as basic Hookean springs to the experimental force-distance relationship. We determine the density of linkers on the nanocrystal surfaces. We demonstrate our method to probe the elastic force of single molecule as a function of chain length. The methodology introduced in this paper opens doors to investigate molecular interactions within organic molecules compressed within a nanocrystal superlattice.