The invention discloses water-based coil steel repair paint and a preparation method thereof. The water-based coil steel repair paint comprises a primer and a finish paint, wherein the primer comprises modified acrylic resin, a pH regulator, a film forming additive, a defoaming agent, a crosslinking agent, an anti-flash rust agent, a surfactant, a mildew preventive, a wetting agent, a thickening agent and water; the finish paint comprises modified acrylic resin, a pH regulator, a film forming additive, a defoaming agent, a dispersant, a crosslinking agent, an anti-flash rust agent, filler, cellulose, a surfactant, a mildew preventive, a wetting agent, a thickening agent and water. The water-based coil steel repair paint has excellent water resistance, alkali resistance and quick drying property, thereby having excellent rust-carrying construction capability as a whole; when the paint is used for coil steel repair, all that is required is that a substrate is treated simply to enable thesurface rust-removing grade to reach Sa1 grade, and coating can be performed with conventional methods such as rolling coating and spraying, so that construction is convenient.