The invention discloses a fluorosilicone resin waterproof colorant and a preparation method thereof, and belongs to the technical field of colorant. The colorant is a semitransparent colored agent andis used for making up for chromatic aberration existing on the surface of a cement base; the colorant comprises the following components by the weight percentage: 10%-50% of an organosilicon emulsion; 1%-10% of a small-molecular permeable material; 1%-10% of a fluororesin emulsion or fluorocarbon modified acrylic emulsion; 5%-40% of an opaque spherical polymer emulsion; 0.1%-1.3% of a catalyst; 2%-10% of a photocatalytic material powder or suspended photocatalyst; 1.2%-2.5% of a defoamer; and the balance water. The problems that a product in the prior art is unable to solidify at room temperature, poor in hardness and wear resistance of a coating layer and unable to decompose pigments and specific binders are solved; the colorant makes visual compensation for the color difference existingon the surface of the cement base so as to achieve color uniformity.