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The understanding and regulation of thermal transport across the solid–liquid interface, especially the electrical double layer (EDL) formed by ionic liquid (IL), is significant for the reasonable design of the efficient thermal dissipation capabilities in the field of chemical engineering. In the present work, by large-scale molecular dynamics simulation method, we reveal that rather than the strong solid–liquid interaction, the atomic structure of EDL dominates the entire interfacial thermal transport across the solid–IL interfaces. The simulation results show that as the surface charge increases, the interfacial thermal resistance (ITR) will decrease in two stages, first sharply and then slowly. The two-dimensional structure factors, the geometry state of cation, and the solid–liquid interfacial energy for different surface charges demonstrate that the evaluation of EDL agrees well with the trend of ITR. Furthermore, the vibrational spectrum and frequency-dependent heat flow also indicate that the high-ordered EDL will enhance the interfacial thermal transport in all frequencies, that is, the high-ordered EDL structure can induce the ultralow thermal resistance and enhance the heat dissipation process. These results also enlightened the future rational design and thermal management of the new IL-based nanoelectrical devices as well as coolants used in the advanced chemical engineering processes, such as supercapacitors, Li-ion batteries, and so forth.