The invention discloses an atomic oxygen protective coating with a physical damage spontaneous repairing function and a preparation method thereof, belonging to the field of spontaneous repairing technology of coatings. The preparation method comprises the steps of firstly, chemically modifying component materials of a traditional atomic oxygen protective coating, deriving chemical groups capableof producing supra-molecular interaction, thereby forming a supra-molecular polymer, with both atomic oxygen protective capability and spontaneous repairing capability, through self-assembling; and then, washing and processing substrate material, and preparing a supra-molecular polymer on the substrate, thereby finishing the preparation of a protective coating described in the invention. The coating provided by the invention has the advantages of good transparency, good atomic oxygen protective effect, strong anti-stripping capability and the like. The coating, after passing through a ground-based simulated atomic oxygen exposure test that approximately runs in a low-earth orbit for half a year, can still maintain good transparency and repairing capability. The atomic oxygen protective coating provided by the invention is simple in process, easily available for materials and low in cost. Therefore, the atomic oxygen protective coating provided by the invention is expected to apply to structural components such as heat insulation materials of spacecrafts, optical elements and flexible substrates of solar panels.