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Understanding how heat flows across interfaces is vital to energy efficiency and thermal stability of many electrical devices. However, the thermal resistance caused by the interface between two materials, termed Kapitza resistance, remains poorly understood. To that end, several first‐principles molecular dynamic simulations and a detailed analysis of the phonon processes and associated transfer of heat at the interfaces of both c‐Si|a‐SiO2 and c‐Si|c‐Ge are presented. It is found that in both cases the interface properties are very important. In the case of c‐Si|a‐SiO2, it is found that interface modes cause inelastic phonon interactions and play a significant role in the total energy transferred. In the case of c‐Si|a‐SiO2, one is able to quantify this effect and find that there is a small set of interface modes which carry >10% of the heat, and decrease the ultimate thermal boundary resistance by 26.5%. [ABSTRACT FROM AUTHOR]