In this paper, we present a novel hybrid numerical-analytical modeling method that is capable of predicting viscoelastic behavior of multiphase polymer nanocomposites, in which the nanoscopic fillers can assume complex configurations. By combining the finite element technique and a micromechanical approach (particularly, the Mori-Tanaka method) with local phase properties, this method operates at low computational cost and effectively accounts for the influence of the interphase as well as in situ nanoparticle morphology. A few examples using this approach to model the viscoelastic response of nanotube and nanoplatelet polymer nanocomposite are presented. This method can also be adapted for modeling other behaviors of polymer nanocomposites, including thermal and electrical properties. It is potentially useful in the prediction of behaviors of other types of nanocomposites, such as metal and ceramic matrix nanocomposites.