Phase-change heat transfer has been demonstrated to be an effective thermal management approach for high-power electronics and power generators. In this work, we propose a strategy using surface functionalization to enhance the phase-change heat transfer of an environmentally friendly refrigerant, i.e., hydrofluoroolefins (HFO)-based R1234yf. Using molecular dynamics simulations, we find that the evaporation (condensation) heat transfer coefficient (HTC) at self-assembled monolayer (SAM) functionalized gold (Au) surfaces can be increased by ∼7 (∼5) times compared to that at the planar Au surfaces. The improvement in phase-change heat transfer of R1234yf at functionalized Au surfaces arises from the high thermal conductance across functionalized Au/R1234yf interfaces and the strong vibrational couplings between SAM molecules and R1234yf molecules. On the one hand, the introduced SAM layer can increase the interfacial thermal conductance (ITC) between Au and R1234yf owing to the strong bonding between Au and the SAM molecules, as well as the strong vibrational couplings at low-frequency modes (0–6 THz) among Au, SAM, and R1234yf. On the other hand, the thermal energy exchange during the evaporation (condensation) process can be improved by surface functionalization through the vibrational couplings between SAM and R1234yf at high frequency (∼12 and ∼30 THz) regions. This dual vibrational coupling will then allow the SAM layer to work as an intermedia to bridge the vibrations between Au and R1234yf molecules, which in return benefits the phase-change heat transfer. By further characterizing the evaporation and condensation processes, we find that the evaporation rate of R1234yf is increased by ∼50% at most at the wall superheat <70 K when the Au surfaces are functionalized using SAMs. When the wall superheat is above 70 K (i.e., 100 K for the planar Au surface), the evaporation of R1234yf becomes like film evaporation in which clusters of R1234yf molecules move off the surface together, which limits the enhancement (i.e., ∼100% at most) of evaporation HTC at the functionalized Au surfaces. At the same time, the condensation rate at functionalized Au surfaces is found to be increased by 15%–100% compared to that of the planar Au surfaces. By elucidating the mechanisms governing phase-change heat transfer on functionalized surfaces, our results provide an efficient strategy to enhance the cooling efficiency of the HFO refrigerants, which may benefit the design of surfaces with high phase-change heat transfer capabilities.