Semiconductor nanocrystals, including their superstructures and hybridized systems, have opened up a new realm to design next-generation functional materials creatively. Their great success and unlimited potential should be largely attributed to surface-adsorbed ligands. However, due to a lack of means to probe and understand their roles in experiments, only a handful of effective ligands have been identified through trial-and-error processes. Alternatively, computational and theoretical methods are ideal for providing physical insights and further guidance. Still, their applications in ligand-coated semiconductor nanocrystals are relatively scarce compared to those of other systems, such as biological chemistry. In this perspective, we first highlight the success of ab initio methods in modeling ligand adsorption. Then, we discuss the opportunities of molecular dynamics and theory in accommodating complex colloidal nature, where we unfold the challenges therein. Finally, we emphasize the need for high-quality force fields to resolve these challenges and look forward to simulation-guided inverse design.