Waterborne epoxy (WEP) nanocomposite coating with hydrothermal synthesized zinc oxide (ZnO)-reduced graphene oxide (RGO)- polypyrrole (PPy) was prepared and an enhanced corrosion resistance was reported. Experiment results showed that WEP nanocomposite coating with Z8R2P (the mass ratio of ZnO-RGO-PPy of 8:2:1) exhibited the highest value of the impedance at the lowest frequency (such as |Z|0.01Hz), the lowest corrosion current density and the largest value of charge transfer resistance (Rct). Even after 94 days of immersion, the |Z|0.01Hz value of Z8R2P/WEP nanocomposite coating was 4.45 × 103 Ω·cm2, pointing out that Z8R2P/WEP coating possessed the long superior anticorrosion performance. Moreover, salt spray experiments with a period of 50 days showed that Z8R2P/WEP coating had the best integrity of coating compared with other coatings, revealing that Z8R2P/WEP coating had the best corrosion protection performance. The characterization and analysis of phase composition and corrosion morphology revealed that the synergistic protection mechanism of Z8R2P/WEP coating was attributed to barrier effects of RGO, chemical passivation of ZnO and accept the released electrons of PPy.