Ever since several formations of polymer-based nanocomposites were reported, research on their modeling, characterization, and computerized analysis methodology has been extensively investigated to become a major academic field of advanced material science and technology. This paper mainly summarizes the multiscale computational analysis methodology for polymer nanocomposites. We also introduce various computational modeling approaches to characterizing the physical behavior of polymer nanocomposites, which are the molecular dynamics approach, and the continuum approach. Based on the various computational analyses, we summarize how the material properties and phenomenological behaviors of polymer nanocomposites were analyzed.