The invention discloses a waterborne epoxy resin emulsion and a preparation method thereof. The preparation method comprises the following steps: heating and dispersing 50-55 wt% of epoxy resin, adding 0.5-1.6 wt% of an alcohol ether solvent and 5.5-6.5 wt% of a composite emulsifier, continuously dispersing, controlling the rotating speed, keeping the temperature, cooling, adding 38-42 wt% of water for phase inversion, and keeping the temperature; and cooling the product, and filtering to obtain the waterborne epoxy emulsion. The two-component room-temperature cured iron oxide red epoxy primerprepared from the waterborne epoxy resin emulsion is an environment-friendly waterborne epoxy anticorrosive coating, the impact resistance of the primer reaches 50 cm, the adhesive force of the primer reaches the first level, and the primer is resistant to water for 300 h and does not blister, peel off, rust or crack; salt fog resistance lasts for 400 h, and foaming, peeling, rusting and crackingare avoided; VOC content is less than or equal to 60 g / L. The waterborne epoxy resin emulsion prepared by the invention is a material with excellent performance.