Interfacial thermal resistance of fillers in thermal conductive polymer composites is a barrier restricting heat dissipation function. In-situ graft of quaternary ammonium group on the surface of graphene can form cation-π interaction, providing a medium for heat transfer between graphene layers. Accordingly, we fabricate polyvinyl alcohol (PVA)-based heat conductive composite containing quaternized graphene stacking structure. With the assistance of non-covalent bonding, the in-plane thermal conductivity of the composite formed by self-precipitation method reaches 9.97 W m−1 K−1 at a filling content of 30 vol%. Molecular dynamics (MD) simulation further explores the promoting effect of the interfacial structure constructed between the charged group and graphene on the interfacial heat transfer. The optimized interfacial structure not only alleviates the bottleneck of interface thermal resistance but also enhances the mechanical properties of composite. This strategy provides an ideal solution to preparation of high-performance thermal management materials for electronic equipment.