In response to the theme of environmental protection and green development in the world in the recent years, waterborne epoxy resin has received more and more attention. Waterborne epoxy resin has lower toxicity, but its low toughness limits the application range of waterborne epoxy resin. Here, we first proposed a method of toughening waterborne epoxy resin with aqueous polyamide salt solution. In this article, a series of waterborne polyamic acid salts is used as modification polymer to improve the high‐temperature resistance and other properties of waterborne epoxy resins by copolymerization modification. Waterborne polyamic acid salt is dispersed uniformly in the epoxy resin. After curing, by compared with the pure epoxy resin, a semi‐interpenetrating network is formed, the cross‐linking density and the high‐temperature resistance of the material are increased, and the glass transition temperature increases from 105°C to 116°C. The storage modulus at 300°C increases from 6.15 to 15.76 MPa. Thermogravimetric Analysis results reveal that the corresponding temperatures of 5% and 10% weight loss increase from 403°C and 419°C to 415°C and 435°C, respectively. At the same time, the toughness of the imide chain segment and polar groups lead to the improved adhesion of the epoxy system, the peeling strength increase from 0.51 to 1.24 N cm−1, and the lap shear strength at high temperature (100°C) increase from 0.58 to 16.97 MPa. The water absorption decreases from 1.51% to 0.66%. The developed waterborne epoxy resin is expected to be used as a high‐temperature waterborne epoxy coating in high‐temperature coatings and other applications.