The invention relates to a water-based color paste for color mixing of a color mixer and a preparation method thereof. The preparation method comprises the following steps: dispersing a surface-modifier-modified organic pigment, a wetting agent, a dispersant, an organic solvent, a rust inhibitor, a moldproof bactericide, polyglycerol fatty acid ester and deionized water, mixing, grinding, filtering, defoaming and the like. The color paste can satisfy the requirements of high moisturizing property, low foam and high storage stability for the water-based color paste.