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 P cr to maintain thermal stability of the junction through efficient dissipation of local heat. We also find that the molecule-probe contact features a powerdependent interfacial thermal resistance R K in the order of 10 9 kW À 1 . Moreover, both P cr and R K display explicit dependence on atomic structures of the junction, force and temperature. For instance, P cr can be elevated in multiple-molecule junctions, and streching the junction enhances R K 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.