With the rapid development of the Chinese marine economy, the anti-corrosion of ships and marine engineering facilities has become urgent to be solved. In this paper, a stable zinc-hydroxyapatite (ZnO-HAP) nanocomposite anti-corrosive pigment was prepared by using the hydrothermal in situ synthesis technique, which supported nano-ZnO onto the hydroxyapatite (HAP) surface. The phase composition, microstructure, and performance of the ZnO-HAP nanocomposite were investigated by X-ray diffraction (XRD), Fourier transform infrared (FT-IR), electron probe microanalysis (EPMA), and electrochemical impedance spectroscopy (EIS), and the anti-corrosion mechanism of the ZnO-HAP nanocomposite was discussed. The results show that the corrosion resistance of the ZnO-HAP/epoxy is better than that of the pure epoxy resin coating. The optimum condition to fabricate ZnO-HAP/epoxy with suitable corrosion resistance was found to be a ZnO/HAP ratio of 0.65/0.35. The synergistic complementation mechanism of ZnO and HAP enriches the metallic anti-corrosion theory and provides a new idea for the synthesis of novel and promising anti-corrosive pigments.