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Replacing solvent-based coatings with waterborne resin ones has become an overall trend in the coating industrial to reduce pollution caused by volatile organic compounds. It is known that introduction of flexibly designable two-dimensional nanoplatelets or zirconium phosphate (ZrP) can improve the mechanical and barrier properties of a film from solvent-based coatings. In this work, we have designed a methodology to prepare nanocomposites for waterborne coating, which consist of waterborne epoxy resin (WER) and polydopamine modified ZrP (PDA-ZrP). It is found that PDA-ZrP has excellent compatibility with WER, and consequently, the film defects of pure WER are fixed. The PDA-ZrP/WER coating exhibits an extremely low corrosion current (1.09 × 10–9 A cm–2) at 1.0% PDA-ZrP loading. It is about 500 times lower than that of the pure WER coating (5.82 × 10–7 A cm–2), and consequently, the same coating has a much smaller rusted area after a salt spray test of 310 h. It should also be noted that all materials we used are eco-friendly, and all experimental procedures are conducted under mild conditions.