The invention discloses high-adhesion water-based waterproof primer as well as a preparation method thereof and application thereof. The high-adhesion water-based waterproof primer is prepared from the following components in parts by weight: 25-32 parts of composite emulsified polymer emulsion, 2.8-3.3 parts of coupling film-forming agent, 0.6-1 part of hydroxyethyl cellulose, 15-18 parts of titanium dioxide, 4-6 parts of barium sulfate, 4-6 parts of calcium carbonate, 4-6 parts of talcum powder, 1-2 parts of dispersing agent, 0.5-1 part of wetting leveling agent, 0.2-0.4 part of de-foaming agent, 0.2-0.3 part of preservative, 1.8-2.2 parts of anti-freezing agent, 0.1-0.3 part of rheological agent, 0.1-0.3 part of pH regulator, 0.4-0.8 part of thickening agent and 24-31 parts of water. The high-adhesion water-based primer has excellent film-forming property, hardness, flexibility, water resistance, chemical resistance, sealing property, seepage force and adhesion, can be effectively dissolved and permeated into an organic silicon mould release agent on novel material plates such as an art ware, a cement product, a glass magnesium board and a special cast sectional material, is inseamless engagement with the board, and achieves the practical effect of improving coating quality and field construction environment. Moreover, the preparation method is easy, is low in cost, is simple in construction way, and reduces production and construction cost.