As a widely used thermal conductive matrix material, the interface problem between polydimethylsiloxane (PDMS) and thermal conductive fillers needs to be solved urgently. The interfacial heat transfer mechanism between PDMS and hexagonal boron nitride (h-BN) modified by different groups was studied by combining density functional theory (DFT) simulation and molecular dynamics (MD) simulation. The bi-functionalization of h-BN was achieved by the environmentally friendly 6-aminocaproic acid (ACA) additive-assisted water ball milling process. The h-BN/PDMS composite thermal interface materials were prepared using a simple rolling method. The thermal conductivity of the obtained sample reached 1.256 W m−1 K−1 at a filler loading of 15 wt%. The proposed bifunctional synergistic heat transfer mechanism is expected to provide theoretical guidance for the preparation of high thermal conductivity and insulating PDMS used in electronic communications.