Ionic liquids (ILs) are a special category of molten salts with melting points near ambient temperatures (or by convention below 100 °C). Owing to their numerous valuable physicochemical properties as bulk liquids, solvents, at surfaces and in confined environments, ILs have attracted increasing attention in both academic and industrial communities in a variety of application areas involving physics, chemistry, material science and engineering. Due to their nearly limitless number of combinations of cation-anion pairs and mixtures with cosolvents, a molecular level understanding of their hierarchical structures and dynamics, requiring strategies to connect several length and time scales, is of crucial significance for rational design of ILs with desired properties, and thereafter refining their functional performance in applications. As an invaluable compliment to experiments from synthesis to characterization, computational modeling and simulations have significantly increased our understanding on how physicochemical and structural properties of ILs can be controlled by their underlying chemical and molecular structures. In this chapter, we will give examples from our own modeling work based on selected IL systems, with focus on imidazolium-based and tetraalkylphosphonium-orthoborate ILs, studied at several spatio-temporal scales in different environments and with particular attention to applications of high technological interest. We start by describing studies performed using ab initio methods on force field development for tetraalkylphosphonium-orthoborate ILs, and computational studies on thermal decomposition of these ILs. The delicate interplay between hydrogen bonding and π-type interactions in an imidazolium-orthoborate IL was studied by performing ab initio molecular dynamics simulations. On the atomistic level, atomistic simulations were performed with constructed force field parameters to study intrinsic molecular interactions between residual water molecules and tetraalkylphosphoniumorthoborate ionic species. For a typical trihexyltetradecylphosphonium bis(oxalato) borate IL at varied concentrations, microstructures and dynamics were systematically analyzed as water concentration increases. The liquid viscosities of typical trihexyltetradecylphosphonium- based ILs were estimated through equilibrium atomistic simulations using Green-Kubo relation with charge scaling factors on ionic species.