Effective thermal management is the key to ensuring lithium-ion batteries (LIBs)’ lifetime and performance. However, the high thermal resistance across the cathode-separator interphase considerably limits the fast heat transfer. Adopting the self-assembled monolayers (SAMs) approach, various organic molecules were selected as the heat controllers to modulate the interfacial thermal conductance (ITC) between the cathode, lithium cobalt oxide (LCO), and the separator, polyethylene (PE). Silane-based SAMs molecules with different groups, including –NH2, –SH, and –CH3, were assembled into the LCO-PE composite’s interphase. Through molecular dynamics (MD) simulations, our results demonstrate SAMs molecules-decorated LCO-PE nanocomposites give a notably improved interfacial heat transfer but are of different magnitude. Such difference mainly results from the different non-bonded interactions and compatibility between SAMs molecules and PE. Of the three SAMs molecules, the assembled 3-aminopropyl trimethoxysilane (APTMS) featuring –NH2 groups improves the ITC the most, about 303.29% in comparison with the pristine interface. Furthermore, these findings help elucidate the underlying mechanisms of how SAMs molecules improve heat transfer across the LCO-PE interphase. Specifically, such enhancement is greatly attributed to the unique SAMs molecules, which build the new heat transfer pathways between LCO and PE, straighten SAMs molecules’ morphology, remove the discontinuities in the temperature field, develop the strong non-bonded interactions between SAMs molecules and PE, and strengthen the coupling vibration of two materials. These investigations provide a new perspective for designing composite’s interphase to mediate the heat transfer and achieve more effective thermal management across the interphase.