The surface treated nano Zr2C by (3-aminopropyl)tris[2-(2-methoxyethoxy)ethoxy]silane (APTMEES) was mixed with graphene oxide (GO), and the resulting GO-APTMEES/Zr2C nanofiller was integrated into the epoxy resin (EP). Electrochemical impedance spectroscopy (EIS), polarization, and scanning electrochemical spectroscopy (SECM) tests were used to evaluate the protection efficiency of epoxy coating on mild steel in the presence of varied concentrations of GO/APTMEES-Zr2C in seawater. The ideal weight proportion of GO-APTMEES/Zr2C in the epoxy matrix was discovered to be 2.0, which resulted in better coating performance. After 1 h of exposure to the marine environment, the coating resistance of EP-GO/ APTMEES-Zr2C was determined to be over 44.9 times higher than that of pure matrix. Even after 180 h in seawater, EIS tests revealed an improved coating resistance of EP-GO/APTMEES-Zr2C nanocomposite (6366.24 kΩ.cm2). Because of the coated substrate’s superior resistance to anodic dissipation, SECM measurements revealed the least discharge of Fe2+ ions at the scratch of the EP-GO/APTMEES-Zr2C coating (1.2 I/nA). Zr2C was found in the rusted components, forming an outstanding inert film at the surface, according to FE-SEM/EDX analysis. The newly produced EP-GO/APTMEES-Zr2C composite had improved barrier properties and hydrophobic characteristics (WCA: 161°), according to the findings. The mechanical characteristics of the epoxy matrix increased when GO-APTMEES/Zr2C was added. As a result, the EPGO/ APTMEES-Zr2C nanocomposite could be used as a coating material for industrial purposes.