Assemblies of 3.5 nm PbS nanoparticles (NPs) nucleate in three dominant superlattice polymorphs: amorphous, body-centered-cubic (bcc) and face-centered-cubic (fcc) phase. This superlattice relationship can be controlled by the inter-NP distance without changing the NP size. Upon increase of inter-NP distance, the packing density decreases, and the capping molecules at NP surfaces change in structure and accordingly modify the surface energy. The driving force for NP assembly develops from an entropic maximization to a reduction of total free energy through multiple interactions between surface molecules and NPs and resulting variation of surface molecules. Upon long-term aging and additional thermal treatment, fcc undergoes a tetragonal distortion and subsequently transforms to bcc phase, and simultaneously, the NPs embedded in supercrystals reduce surface energy primarily in {200} facets. Linking molecule-NP interactions with a series of changes of packing density and surface lattice spacings of NPs allows for an interpretation of principles governing the nucleation, structure stability, and transformation of PbS NP-assembled supercrystals.