The invention relates to a water-based heavy-duty single-component primer, which is prepared from the following components in parts by mass: 18 to 33, preferably 20 to 30, parts of de-ionized water, 1.5 to 10, preferably 2 to 8, parts of a coalescing agent, 6 to 12, preferably 8 to 10, parts of an anti-rust pigment, 3.5 to 17, preferably 5 to 15, parts of filler, 0.3 to 1.2, preferably 0.5 to 1.0, part of a dispersant, 0.08 to 0.4, preferably 0.1 to 0.3, part of a pH regulator, 38 to 75, preferably 40 to 70, parts of a film former, 7 to 11, preferably 8 to 10, parts of a complexing agent and 0.1 to 0.3, preferably 0.2, part of a penetrant. The invention also provides a preparation method and application of the water-based heavy-duty single-component primer.