The properties of interphase in polymer composites are often different from those of bulk polymer matrix, which may include chemical, physical, microstructural, and mechanical properties. The nature of interphase is critical to the overall properties and performance of polymer materials, in particular in nanofiller reinforced composites. Experimental efforts have been made to determine the effective interphase thickness and its properties, for example, by nanoindentation and nanoscratch techniques. Yet, it is very difficult to quantify the interphase and its properties because of its nanoscale nature and the unclear boundary. In this regard, computer simulation, e.g., molecular dynamics, provides an effective tool to characterize such interphase and the properties. In this work, molecular dynamics simulations are applied to quantify the interphase thickness in clay-based polymer nanocomposites. Then, the mechanical properties of the so-called effective nanofiller (i.e., the physical size of nanofiller plus the thickness of interphase) will be determined by a series of simulations.