Self-assembling of nanocrystals involves organization of nanocrystals encapsulated by protective compact organic molecules into a crystalline material. The adsorbed molecules not only serve as the protection layer for the nanocrystals but also provide the dominant cohesive interactions (or "bonding") sustaining the nanocrystal superlattices. The length of the adsorbed molecules is a controllable parameter, making the ratio of particle size to interparticle distance an adjustable parameter that sensitively tunes the interparticle interaction/coupling and resulting collective properties. In this paper, bundling and interdigitation of thiolate molecules adsorbed on Ag nanocrystals are observed using the chemical imaging technique in energy-filtered transmission electron microscopy (EF-TEM) at a resolution of similar to 2 nm. In these orientationally ordered, self-assembled Ag-nanocrystal superlattices, the bundling of the adsorbed molecules on the nanocrystal surfaces is the fundamental structural principle. A model consistent with the nanocrystal＇s morphology and the interdigitation of the adsorbed thiolates is proposed.