The invention relates to the technical field of coatings, in particular to a water-based inorganic nano-composite silicon resin anticorrosive coating and a preparation method thereof. The coating comprises the following components in parts by weight: 60-75 parts by weight of epoxy modified organic silicon resin, 20-40 parts by weight of fluorocarbon elastic emulsion, 25-50 parts by weight of modified nano silicon dioxide sol, 10-20 parts by weight of nano garnet, 5-15 parts by weight of grinding wheel ash, 1-10 parts by weight of a dispersing agent, 1-10 parts by weight of a coalescing agent, 0.5-5 parts by weight of a defoaming agent, 0.5-5 parts by weight of a flatting agent, 0.5-5 parts by weight of a thickening agent and 50-65 parts by weight of deionized water. The water-based inorganic nano-composite silicon resin coating prepared by the invention is rapidly cured at low temperature, so that the coating not only has higher hardness and adhesive force, but also has excellent corrosion resistance, water resistance, stain resistance, impact resistance, wear resistance, heat resistance and weather resistance; and the coating can be widely applied to corrosion prevention of marine buildings and marine equipment.