The understanding of interfacial heat transfer mechanism is increasingly significant since interfacial thermal resistance plays an important role in thermal management as the size of electronic devices decreases. In this work, interfacial heat transfer between five diverse silica surfaces and two organic liquids was studied using the molecular dynamics method. The two organic liquids are triacontane and triacontanol, which are either hydrogen bond incapable or capable, respectively. Silica surfaces with silanols show better thermal transport ability with triacontane/triacontanol because of a vibration matching effect. Increase of silanol area number density enhances the interfacial heat transfer for silica–triacontanol systems but has little effect for silica–triacontane systems because triacontane is hydrogen bond incapable. However, even for silica–triacontanol, the improvement of interfacial heat transfer does not scale proportionally to silanol area number density, since silanol–triacontanol and silanol–silanol hydrogen bonds are competing. The effective hydroxyl density is proved to reasonably explain this effect. Furthermore, temperature affects the interfacial heat transfer of silica-triacontanol systems vitally because both the number and lifetime of hydrogen bonds are reduced at higher temperature. The vertical orientation of triacontanol adsorbed onto the interface brings efficient heat paths via hydrogen bonds and alkyl backbones, which causes the interfacial molecular layers of triacontanol to have higher thermal conductivity in the direction normal to the interface.