This study investigated the functionalization and layer number effects on interfacial thermal conductivity (ITC) of graphene nanocomposites through molecular dynamics simulation. The functional groups grafted to the graphene surface were carboxyl and amine groups. The ITC between the graphene and the surrounding epoxy matrix was examined, and the effects of the functional groups and layer number on ITC were characterized through vibrational density of states (VDOS). It was revealed that the VDOS mismatch between the epoxy and the outermost layer of graphene was reduced by the functional groups. Thus, the functional groups can effectively improve the ITC between the graphene and epoxy matrix. Moreover, when the layer number of graphene increases, the ITC in nanocomposites increases correspondingly. This is attributed to the fact that the inner layers of graphene may interact with the epoxy matrix and contribute the interatomistic energy in the interface.