This study explores the critical role of nonpolar ligand-solvent systems in modulating interparticle interactions in colloidal nanocrystals, profoundly affecting colloidal stability and enabling precision self-assembly. A library of 28 ligands with diverse molecular fragments─double bonds, branched chains, benzene rings, and naphthalene rings─and four solvents was developed to investigate how fragment types and positions affect ligand ordering and interparticle attraction. Explicit solvent simulations with enhanced sampling techniques reveal that fragments near the headgroup or midsection disrupt ligand ordering and weaken interparticle attraction, whereas terminal placement fosters ordered ligand packing and enhances attraction. Simulation predictions on the relationship between ligand structures and interparticle interactions were validated through self-assembly experiments using colloidal nanocrystals passivated by six representative ligands. Furthermore, the potential to control ligand ordering and interparticle interactions was demonstrated by tuning fragment types, positions, combinations, and solvent sizes. This work deepens the understanding of ligand-solvent dynamics and provides a theoretical framework for the molecular-level design of nanocrystal self-assembly.