The invention relates to the field of chemical anti-corrosion coatings, particularly to a water-based rust-proof primer with rust and a preparation method thereof. The water-based rust-proof primer with rust uses a vinyl emulsion, a core-shell-structured acrylic emulsion and a phosphate-modified acrylic acid emulsion as base materials. The preparation method comprises the following steps: firstly,selecting the main base material, i.e., the vinyl emulsion; then synthesizing the auxiliary base materials, i.e., the core-shell-structured acrylic resin emulsion and the phosphate-modified acrylic emulsion; and then with the above three emulsions as the base materials, mixing the base materials with a rust conversion agent, an antifreezing agent, a wetting agent, an antifoaming agents and otheradditives to prepare the water-based rust-proof primer with rust. The obtained water-based rust-proof primer with rust is low in VOC content, safe and environment-friendly, convenient to construct, good in compatibility with common anti-corrosion topcoats, good in rust conversion effect, strong in adhesion and long in an antirust period, and has wide application prospects.