The work aims to prepare a new green epoxy resin composite coating system by functionalized composite of two-dimensional nanomaterial, graphitic phase carbon nitride (g-C3N4), and the natural polymer chitosan (CS), and study the effect of different g-C3N4@CS additions on the corrosion resistance of the epoxy composite coating, so as to ensure the green, environmental protection and efficient corrosion resistance of water epoxy resin (EP) coating. The g-C3N4 was obtained by high-temperature calcination of urea, which was added into chitosan suspension for modification treatment to obtain the novel nanofiller g-C3N4@CS. g-C3N4@CS with different mass fractions by doping into the epoxy resin. The structures and microscopic morphologies of g-C3N4 and g-C3N4@CS composites were characterized by Fourier Transform Infrared Spectroscopy (FT-IR), X-ray Diffractometer (XRD), and Transmission Electron Microscopy (TEM). The corrosion resistance of the composite coating system was tested by electrochemical methods and long-term socking experiments. Combining the adhesion test of the coating, the adhesion between the coating and the substrate was determined. The results showed that g-C3N4@CS could be successfully compounded into the EP coating. The abundant oxygen-containing functional groups in CS could effectively improve the dispersion and interface compatibility of g-C3N4 in epoxy resin. Electrochemical impedance spectroscopy test results indicated that the coating resistance (Rc) value of EP/g-C3N4@CS-1.0wt.% coating system was the largest after 30 d of immersion, and it could still reach 1.11×107 Ω after 30 d of immersion. The EP/g-C3N4@CS-1.0wt.% coating system had the highest corrosion resistance. In addition, g-C3N4@CS could significantly improve the adhesion of EP coatings, and the EP/g-C3N4@CS-1.0wt.% coating had the highest adhesion. The results of long-term immersion test also showed that the surface film of the EP/g-C3N4@CS-1.0wt.% coating system had the best corrosion resistance and the surface film was still uniform and flat after 30 days of immersion. The uniform and complete composite film formed by the EP/g-C3N4@CS-1.0 wt.% coating system can effectively shield the migration process of corrosive ions and has the best corrosion resistance.