The invention discloses water-based environmentally-friendly epoxy anti-corrosion primer and a preparation method thereof. The water-based environmentally-friendly epoxy anti-corrosion primer comprises water-based epoxy resin emulsion, fluorocarbon emulsion, filler, rust-proof pigment, deionized water, a silane coupling agent, preservative, ketimine resin, water-based epoxy hardener, flake mica powder, titanium dioxide, a dispersing agent, accelerator, a flattening agent, a defoaming agent, wetting dispersant, talcum powder, fatty amine, a penetrating agent, sticky rice powder, rhizoma bletillae, poria, folium artemisiae argyi and herba centipedae. The water-based environmentally-friendly epoxy anti-corrosion primer is high in drying speed, good in corrosion resistance and rust resistance, good in heat-resistant stability, low in VOC emission, good in binding power, high in strength, free of heavy metal such as chromium and free of pollution; traditional Chinese medicine components including the rhizoma bletillae, the poria, the folium artemisiae argyi and the herba centipedae are further added, after the water-based environmentally-friendly epoxy anti-corrosion primer is used, the traditional Chinese medicine components can be emitted continuously towards a room and enter the human body through the respiratory tract, the skin and the mucosa, the smell is fresh, and air purifying and antibacterial and bactericidal effects are achieved.