A physics-based nested hierarchical approach is established to investigate thermal conducting behavior of micro-filler (in the form of particle, short and long fiber)/nanoparticle-reinforced polymer hybrid nanocomposites. An effort is made to develop a unit cell-based micromechanical model predicting the thermal conductivities of general composite systems, including microscale filler-reinforced composites, nanoparticle-reinforced nanocomposites and microscale filler/nanoparticle-reinforced hybrid nanocomposites. The role of the nanoparticle/polymer interfacial thermal resistance is also considered in the analysis. The developed model presents a reasonable behavior compared with available experiments and other modeling methods for the thermal properties of composites and nanocomposites. The results are provided for two types of hybrid nanocomposites, including carbon micro-filler/silica (SiO2) nanoparticle-reinforced epoxy and glass micro-filler/SiO2 nanoparticle-reinforced epoxy systems. It is found that transverse thermal conducting behavior of general fibrous composites is significantly affected by adding the nanoparticles. However, due to the dominated role of the carbon fiber in the longitudinal direction, the longitudinal thermal conductivity of carbon fiber-reinforced composites is not influenced by the nanoparticles. Also, the thermal conductivities of both randomly oriented short fiber-reinforced composite and particulate composite systems can be improved with the addition of the nanoparticles. The obtained results could be useful to guide the design of hybrid nanocomposites with optimal thermal conductivities.