Novel waterborne acrylic resin modified with glycidyl methacrylate (GMA) was successfully synthesized via homogeneous solution polymerization in isopropyl alcohol followed by solvent exchange with water. Aminopropyltriethoxysilane (KH-550), a silane coupling agent that can crosslink with resin and iron base material, was used as curing agent for solidifying this GMA modified resin. The cured mechanism of the coating was also investigated by 29Si nuclear magnetic resonance (29Si NMR) spectra and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). The waterborne acrylic resin was sprayed on the iron base material and cured by KH-550 for 30 min at 100 °C to form the desired coating. The GMA and KH-550 were found to significantly decrease the curing temperature of this two-component waterborne resin. The thermal property of the coatings with different GMA loadings was investigated using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The GMA enhanced the thermal stability of the coatings from 100 to 400 °C. The modification of GMA was found to reinforce significantly the mechanical properties of the coatings. The tensile strength of coating modified with 15 wt% GMA got a 78.65% improvement compared to that of unmodified resin. The surface hydrophobicity of the coatings does get affected by this modification. The contact angle got increased from 87.72°of the unmodified resin coating to 99.51°of coating modified with 15 wt% GMA. This work opens a new way to synthesize high performance waterborne acrylic resin and reports on the anti-flash corrosion of waterborne coatings on the iron base material surface.