The invention discloses a water-based permeable self-healing high polymer modified asphalt waterproof coating with a hydrophobic surface as well as a preparation method and application thereof. The coating is prepared from emulsified asphalt, acrylate emulsion, an alkali swelling thickener, a polyurethane thickener, a dispersing agent, a multifunctional additive, a defoaming agent, a sterilizing agent, ground calcium carbonate powder, bentonite, an organic silicon water repellent, sodium silicate, a photoinitiator, a cross-linking agent and water. The coating disclosed by the invention mainlyhas rapid curing performance, self-healing performance, ultrahigh bonding strength and elongation rate and excellent water resistance and high and low temperature resistance, is suitable for various environments, can achieve a good waterproof effect on a building structure in any environment, is particularly suitable for waterproof engineering of various extremely complex environments, projects ofsome complex scenes and some special regions and projects, fills the blank of the material in severe cold regions, and is wide in application range.