The uniform dispersion and compatibility of hydrophobic polyaniline (PANI) and reduced graphene oxide (RGO) in waterborne polymer matrices always remain a key challenge. Here, cationic gemini surfactant (CGS) was used as an intercalation agent to modify RGO, and simultaneously functionalized as a dopant to assist in situ chemical oxidation polymerization of aniline on CGS modified RGO (CGG) nanosheets to prepare CGG/PANI nanocomposite. The conventional hexadecyl trimethyl ammonium bromide (CTAB) surfactant with the same structural unit as CGS was also utilized to prepare CTAB modified RGO (CTG) and CTG/PANI nanocomposite. The resulting CGG/PANI and CTG/PANI nanocomposites were added into waterborne alkyd resin (WAR) as nanofiller to prepare anti-corrosion coatings. Compared with CTAB, higher content of CGS was intercalated into the RGO nanosheets, resulting in the higher interlayer spacing of CGG. It is beneficial for the uniform chemical deposition of PANI on CGG via in situ polymerization of aniline. The CGG/PANI/WAR and CTG/PANI/WAR nanocomposite coatings displayed significantly improved adhesion, water resistance and hardness in comparison with the pristine WAR and PANI/WAR coatings. Compared with WAR coating, the corrosion current density of CGG/PANI/WAR nanocomposite coating decreased by three orders of magnitude, and the corrosion potential shifted from −0.782 V to −0.225 V. The impedance modulus of WAR, CTG/PANI/WAR and CGG/PANI/WAR nanocomposite coatings were found to be 1.56 × 105, 5.12 × 107 and 4.15 × 108 Ω·cm2, further demonstrating the significantly improved anti-corrosion properties. The anti-corrosion efficiency CGG/PANI/WAR reached 98.63 %, which was higher than that of CTG/PANI/WAR (95.35 %). Moreover, the electrochemical impedance spectroscopy and salt spray test displayed the enhanced long-term anti-corrosion properties for CGG/PANI/WAR nanocomposite coating, certifying the Gemini surfactant is more effective in fabricating a synergistic waterborne [email protected] system of enhanced anti-corrosion properties.