With the rise of atomic-scale devices such as molecular electronics and scanning probe microscopies, energy transport processes through molecular junctions have attracted notable research interest recently. In this work, heat dissipation and transport across diamond/benzene/diamond molecular junctions are explored by performing atomistic simulations. We identify the critical power Pcr to maintain thermal stability of the junction through efficient dissipation of local heat. We also find that the molecule–probe contact features a power-dependent interfacial thermal resistance RK in the order of 109 kW−1. Moreover, both Pcr and RK display explicit dependence on atomic structures of the junction, force and temperature. For instance, Pcr can be elevated in multiple-molecule junctions, and streching the junction enhances RK by a factor of 2. The applications of these findings in molecular electronics and scanning probing measurements are discussed, providing practical guidelines in their rational design.