The invention discloses a modified epoxy resin emulsion and a preparation method thereof. The preparation method comprises the steps of carrying out chemical reaction by virtue of epoxy resin, glycidyl ether and organic amine containing two active hydrogen so as to generate water-soluble modified epoxy resin with a hydrophilic chain segment, adding water, and preparing the modified epoxy resin emulsion under a high-speed shear dispersion effect. According to the modified epoxy resin emulsion, water is taken as a dispersion medium, so that the modified epoxy resin emulsion does not contain an organic solvent, is safe in use and can meet the environment-friendly requirement, and the environmental pollution is avoided. The modified epoxy resin emulsion is matched with a waterborne epoxy curing agent and can be constructed and cured in various environments, and a cured product is flexible and weather-resistant, has good adhesiveness with various base materials and is capable of defensing the corrosion of water and common chemical mediums.