Novel N-doped carbon nanonet flakes (NCNFs), consisting of three-dimensional interconnected carbon nanotube and penetrable mesopore channels were synthesized in the assistance of a hybrid catalytic template of silica-coated-linear polyethyleneimine (PEI). Resorcinol-formaldehyde resin and melamine were used as precursors for carbon and nitrogen, respectively, which were spontaneously formed on the silica-coated-PEI template and then annealed at 700 °C in a N2 atmosphere to be transformed into the hierarchical 3D N-doped carbon nanonetworks. The obtained NCNFs possess high surface area (946 m2 g−1), uniform pore size (2–5 nm), and excellent electron and ion conductivity, which were quite beneficial for electrochemical double-layered supercapacitors (EDLSs). The supercapacitor synthesized from NCNFs electrodes exhibited both extremely high capacitance (up to 613 F g−1 at 1 A g−1) and excellent long-term capacitance retention performance (96% capacitive retention after 20,000 cycles), which established the current processing among the most competitive strategies for the synthesis of high performance supercapacitors.