gaps is of critical importance for their performance. Interfacial thermal resistance arises from the mismatch between vibrational modes in the contact materials [4] and weak interactions between them at the interface. [5] The resistance could be reduced by introducing thermal interface materials (TIMs), which fill the gap between materials and enhance the interfacial thermal coupling. A characteristic length scale [6] for interfacial thermal transport could be defined as l I = κ/G, where κ is the thermal conductivity of materials on two sides of the interface, and G is the interfacial thermal conductance (ITC). The interfacial thermal resistance R = 1/G could be neglected for thermal transport over a distance that is much longer than l I . Accordingly, we can define the thermal transparency as λ = L/l I , where L is the thickness of the interface or the TIM. On the other hand, soft TIMs with structural flexibility are beneficial for geometrical compatibility between rough surfaces and structural robustness under external perturbations. One can measure the structural flexibility of a TIM by Y −1 , where Y is the Young's modulus. A combination of high thermal transparency and structural flexibility makes a TIM versatile in practical applications. In recent studies, polymers and nanostructures such as carbon nanotubes and graphene sheets have been explored as potential TIMs with these merits. [6,7] It has been reported that polymer chains exhibit high thermal conductivity along the chain direction if the orientational order is preserved as in the crystalline phase (≈130 W m −1 K −1 for polyethylene), which hold great promises in thermal management applications. [8] Linear molecules such as alkane chains could also arrange themselves into self-assembled monolayers (SAMs) on various substrates, [9] which feature certain orientational order and entropy-controlled soft elasticity, and have been proposed for applications that range from molecular electronics, [1] thermoelectric materials, [10] thermal management, [9a,11] to interfacial functionalization for enhanced thermal transport. [5,12] Thermal and mechanical properties of SAMs have been explored both experimentally and theoretically as potential TIMs. [4,5,13] Zheng et al. [14] showed that silane-based SAMs with varying end groups enhance the ITC between sapphire and poly styrene by a factor of 7, through functionalizing the sapphire surface with SAM. Acharya et al. [15] calculated the thermal conductance of silicon-SAM-water interfaces through Thermal interface materials (TIMs) are highly desirable for efficient thermal transfer or dissipation in a wide range of material and device applications. The self-assembled monolayers (SAMs) are promising candidates for these applications due to their high thermal transparency and structural flexibility. In this work, the performance of SAMs as practical TIMs is assessed by performing atomistic simulations. The mixed nature of diffusive and ballistic thermal transport is identified across the monolayers from signatures ...