The invention discloses a composite nano coating and a preparation method thereof and relates to the field of coatings. The formula of the composite nano coating comprises raw materials and auxiliaries, the raw materials include an aqueous amino-acid resin, an aqueous epoxy resin, nano ion silver and nano fumed silica, and the auxiliaries include a parting agent, a flatting agent, a dispersing agent, an adhesive agent, an antifoaming agent, purified water and alcohol. The preparation method of the composite nano coating includes weighing water borne polyurethane and the aqueous epoxy resin based on requirements, mixing the water borne polyurethane and the aqueous epoxy resin to obtain a mixture, dispersing the mixture for 5-15 minutes by a high-speed dispersion machine, adding a certain amount of the nano ion silver, the parting agent, the flatting agent, the dispersing agent, the adhesive agent and the antifoaming agent, dispersing for 10-30 minutes, removing bubbles, adding the nano fumed silica and the parting agent, adding a certain amount of the water and the alcohol after the dispersion, fully dispersing for 30-50 minutes, and performing a nanoscale sanding. The composite nano coating has the advantages that the coating adhesive force and the thermal conductivity are high, and the coating is corrosion resistant and has a hydrophobic effect.