Creating covalent bonds between inorganic fillers and polymer matrix is an effective method to enhance the thermal conductivity (TC) of composite materials, while the detailed mechanism is still not clear. By introducing different silane coupling agents (SCAB) bonding poly(vinyl alcohol) (PVA) and functionalized boron nitride (fBN), intrinsic relationship between molecular structure of silane crosslinkers and TC of PVA-fBN composite has been systematically investigated. The results show that the SCAB molecules with short side chain, i.e. vinyl triethoxysilane (VTES) and tetraethyl orthosilicate (TEOS), increase the TC of composite polymer, with maximum value of 1.636 W/m.K, which is 337.3% of that of PVA/fBN. In contrast, 3-glycidoxypropyltrimethoxy silane (GPTMS) with long side chain decreases the TC to 54.4% of that of PVA-fBN. The number of hydrolyzable Si-O-R of SCAB molecules affects the TC of PVA-fBN composite through controlling the self-condensation degree of SCAB. Integrated with atomistic simulations, these findings provide new insights for the design of polymer-based thermal management materials.