The energy performance of nanothermites in aqueous conditions is commonly restricted by the rapid heat dissipation and corrosion of nano-Al. Here we report studies on the fabrication and submerged ignition for the super-hydrophobic nanothermite film based upon the Co3O4/Al core/shell nanowires (NWs). The Co3O4 NWs arrays, which are synthesized using a facile hydrothermal-annealing method, serve as templates for the deposition of Al shells by magnetron sputtering. The super-hydrophobic surface is subsequently realized by the fluoroalkylsilane coating. The tests of the laser-induced underwater ignition reveal that the super-hydrophobic modification effectively could lead to the ignition of the nanothermite film. Furthermore, the anti-aging behaviors of the obtained super-hydrophobic nanothermite film in aqueous conditions are investigated in detail to compare the heat-release and ignition characteristics at different submersion times. Impressively, the resultant super-hydrophobic composite could still hold about 50% of the original energy even after an underwater storage of 2 days.