The invention particularly relates to a water-based polycarbonate-modified silica sol composite paint and a preparation method thereof, belonging to the technical field of paints. The composite paint comprises the following components: a polycarbonate-modified silica sol, an organic silicon aid, a dispersing agent, rutile titanium white, talcum powder, ground calcium carbonate, calcined kaolin, a film forming aid, a wetting agent, a first thickener, a second thickener, a first defoaming agent, a second defoaming agent, an antifreezing agent, a mildewproof bactericide and the balance of deionized water. The water-based polycarbonate-modified silica sol composite paint has excellent comprehensive properties: the hardness of the coating can reach 7H, the adhesive force of the coating is Grade 01, the scrub resistance exceeds 12000 times, and the pollution resistance is 7.9%. Meanwhile, the coating of the water-based polycarbonate-modified silica sol composite paint has the advantages of uniform surface arrangement and smooth surface, and all the components have favorable dispersion effects and basically do not have the phenomenon of aggregation.