Graphene has been extensively applied in composite materials due to its high thermal conductivity. Multi-layered graphene has great potential in the construction of a continuous filler network but is restricted by the high interfacial thermal resistance between adjacent graphene layers. This paper investigates the effects of the overlapping area and interlayer sp3 bonding of partially overlapped bilayer graphene on the interfacial thermal resistance using molecular dynamic simulations. The results show the linear relationship between the interfacial thermal resistance and the overlapping area. Then, identical vacancy defects of the same plane coordinates were added to each of the two graphene sheets, and it was found that the presence of an armchair edge restricted the formation of interface sp3 bonding to some extent, while the zigzag edge did not. However, their similar bond length and the phonon density of state of bonded atoms in the models with different edges indicated their similar effects on the heat transfer. Therefore, the thermal resistance of all single sp3 bonds in different models could be approximated to 14.3 × 10-9 m2 KW-1. A formula is proposed to describe the inverse relationship between the number of sp3 bonds and the interfacial thermal resistance. Finally, the vacancy defect on the upper graphene sheet was moved to stagger the two vacancies. The length of sp3 bonds was changed slightly due to the staggered arrangement, and the interfacial thermal resistance was found to be positively correlated with the bond length. This allows valuable interfacial heat-transfer properties of the partially overlapped bilayer graphene to contribute to the thermal management of the 3D filler network.