Structure-guided combustion wave (SGCW) which is induced by combustion waves at the interfaces of chemical fuel and micro-nanostructures is a facile fabrication method to manipulate the physicochemical properties of target materials and to form carbon shell surrounding them. In this work, the carbon shells, fabricated by SGCWs are used as conductive coating layers on metal oxide nanoparticles or templates for coating thin metal oxide layers through a hydrothermal reaction using oxidizers such as KMnO4. Two novel core-shell nanostructures, MnO2-x@carbon (C) and TiO2@MnO2@C were synthesized via SGCWs to study the underlying mechanism of carbon-shell formation and to demonstrate the scalability of these approaches. Furthermore, the fabricated core-shell structures of transition metal oxides and carbon layers were applied as active materials in supercapacitors, and they showed highly improved specific capacitance and cycling stability due to the presence of carbon shells and the optimization of micro-nanostructures during the application of SGCWs.