The invention discloses an epoxy modified acrylic emulsion and a preparation method thereof. The epoxy modified acrylic emulsion comprises three components A, B and C, wherein the component A comprises deionized water, an emulsifier, epoxy resin, an acylamino compound, styrene, acrylate, methacrylate and (meth)acrylic acid; the component B comprises deionized water, a buffer agent and an emulsifier; the component C comprises deionized water and an initiator; in the emulsion system, a reducing agent, protective glue, a functional monomer, a neutralizing agent and the like can also be included.The prepared emulsion has the characteristics of fine granules, good elasticity, light resistance, weather resistance, water resistance and the like, and can be applied to waterborne industrial coating, waterborne building coating and waterborne wood coating. The waterborne coating prepared from the emulsion provided by the invention has the characteristics of strong adhesion, high mechanical properties, low curing shrinkage, good water/oil resistance, good temperature change resistance, good heat resistance, excellent aging resistance, excellent electrical insulation, excellent chemical resistance and the like.