Efficient thermal management is very critical for the performance and longevity of modern electronic devices, making the development of high thermal conductivity materials essential. In this work, the effect of nanoparticle/nanosheet hybrid fillers on the thermal conductivity of polymer nanocomposites (PNCs) was explored by using coarse-grained molecular dynamics (CGMD) simulation. First, the effects of nanosphere fillers on the conductivity of composites were studied in terms of filling fraction, size, and physical interfacial interaction. The results show that the maximum probability is achieved with a smaller particle size, a larger filling fraction, and a stronger matrix-filler interaction. In addition, we further examined the thermal performance of nanoparticle/nanosheet hybrid-filled composites, the dispersion state of the fillers, and the contribution of the two filler components to the formation of a thermal conductivity network. Compared with PNCs with a single type filler, PNCs filled with nanoparticles/nanosheets exhibit superior thermal conduction probability and a lower percolation threshold, which is attributed to the fact that the addition of nanoparticles promotes the dispersion of the sheets and the formation of conductivity networks. By controlling the size, filling fraction, and filler-matrix interaction of the nanoparticles, the thermal conduction probability of the composites can also be modified. In conclusion, this study deepens our understanding of how to form a thermal conductivity network between nanoparticles and sheets, providing theoretical guidance for the development of more efficient thermal conductivity polymeric materials.