The invention relates to a water-based anticorrosive coating with rust and a preparation method thereof. The water-based anticorrosive coating with the rust comprises the raw materials: 22-35 parts of de-ionized water, 35-45 parts of a fluorine-containing emulsion with the rust, 1-3 parts of an additive, 8-13 parts of an antirust pigment, 1-3 parts of color paste, 5-10 parts of filler, 2-8 parts of a transforming agent or a rust stabilizing agent, and 1.5-3.5 parts of an anti-settling agent, wherein the fluorine-containing emulsion with the rust is a coreshell emulsion prepared from a monomer, an emulsifying agent and an initiating agent; the emulsifying agent comprises the components of a phosphate emulsifying agent and a sodium sulfonate emulsifying agent; a shell part comprises the transforming agent or the rust stabilizing agent. The preparation method comprises the following steps of: stirring part of the de-ionized water, the additive, the transforming agent or the rust stabilizing agent, the anti-settling agent, the antirust pigment and the filler, and grinding the mixture into slurry; adding the fluorine-containing emulsion with the rust and the like while stirring to prepare the anticorrosive coating with the rust. The coating is nontoxic, odorless, non-combustible, non-explosive, non-volatile and low in VOC (volatile organic compounds), can be used for replacing a derusting and descaling process; a protective primer with a high adhesion force is formed; a conventional derusting process can be replaced; the coating can be directly applied to a steel structure or maintenance engineering of mechanical equipment.