Understanding the physical properties of ionic liquids (ILs) via computer simulation is important for their potential technological applications. The goal of our IL research is to obtain a unified understanding of the properties of ILs with respect to their underlying molecular structure. From atomistic molecular dynamics simulations, the many-body electronic polarization effect was found to be important for modeling ILs, especially their dynamics. The multiscale coarse-graining methodology has also been employed to increase the simulation speed by a factor of 100 or more, thereby making it possible to study the mesoscopic behavior of ILs by computer simulations. With these simulation techniques, ILs with an amphiphilic cation were found to exhibit a spatial heterogeneity due to the aggregation of their nonpolar alkyl tails. This spatial heterogeneity is a key feature in interpreting many physical phenomena of ILs, such as their heterogeneous self-diffusion and surface layering, as well as their surfactant-like micelles formed in IL/water mixtures.