Polyaniline (PANI), as a conductive polymer, has been widely used in the corrosion protection of polymer coatings due to its high electrical conductivity and passivation effect. However, the agglomeration tendency and the difficulty of dispersion in the polymer hinder the anti-corrosion properties of PANI fillers. Therefore, in this paper, PANI nanorods were in situ polymerized on the surface of nitrogen and fluorine dual-doped graphene oxide (NFGO) layers to prepare PANI/NFGO composites and used to improve the anti-corrosion performance of waterborne epoxy coatings. The doped N elements and CF conformation with semi-ionic C−F bonds in NFGO enhanced the electrical conductivity and modified the graphene electric cloud distribution to form a fast conductive pathway in the graphene layer. In addition, the oxygen-containing groups in NFGO provided a site for the polymerization of PANI nanorods and enhance their hydrophilicity and dispersibility. Besides the capability of filling the micro-pores in the coating, the large specific surface area, the high electrical conductivity of NFGO, and the compact junction with PANI enable the electron transfer in a larger area, which increases the area of the inhibitor layer and ultimately enhanced the anticorrosion performance. The corrosion resistance performance was investigated via electrochemical impedance spectroscopy (EIS) and salt spray tests. PANI/NFGO/WEP showed the highest corrosion resistance in EIS with the R ct value of 1.213 × 10 10 Ω cm 2 , which was more than one order of magnitude higher than WEP. The excellent anti-corrosion properties were due to the synergistic effect of the physical properties of NFGO and the passivation effect of PANI nanorods.