The use of hybrid fillers consisting of phycochemically different nanoparticles has been widely investigated to realize synergistic improvement of thermal conduction behaviors. The enhancement of thermal conductivity of composites is often limited by the thermal contact resistance of the reinforcing particles. We prepare a series of hybrid nanofiller reinforced composites composed of two-dimensional boron nitrides and one-dimensional multiwalled carbon nanotubes to investigate the interfacial thermal resistances of the composites by a finite element method. The interfacial thermal resistances calculated by the finite element modeling are implemented into a Mori–Tanaka homogenization scheme to predict the thermal conductivities of the composites with perfect and imperfect interfaces. The prediction by the Mori–Tanaka method was in good agreement with the finite element simulation and the experimental results.