Two mechanisms that enhance heat dissipation at solid-liquid interfaces are investigated from the atomistic point of view using nonequilibrium molecular dynamics simulation. The mechanisms include surface functionalization, where –OH terminated headgroups and self-assembled monolayers (SAMs) with different chain lengths are used to recondition and modify the hydrophilicity of silica surface, and vibrational matching between crystalline silica and liquid water, where three-dimensional nanopillars are grown at the interface in the direction of the heat flux with different lengths to rectify the vibrational frequencies of surface atoms. The heat dissipation is measured in terms of the thermal conductance of the solid-liquid interface and is obtained by imposing a one-dimensional heat flux along the simulation domain. A comparison with reported numerical and experimental thermal conductance measurements for similar interfaces indicates that the thermal conductance is enhanced by 1.8–3.2 times when the silica surface is reconditioned with hydrophilic groups. The enhancement is further promoted by SAMs, which results in a 20% higher thermal conductance compared with that of the fully hydroxylated silica surface. Likewise, the presence of nanopillars enhances the interface thermal conductance by 2.6 times compared with a bare surface (without nanopillars). Moreover, for different nanopillar densities, the conductance increases linearly with the length of the pillar and saturates at around 4.26 nm. Changes in the vibrational spectrum of surface atoms and water confinement effects are found to be responsible for the increase in conductance. The modification of surface vibrational states provides a tunable path to enhance heat dissipation, which can also be easily applied to other fluids and interfaces.