In this study, ZnAl-layered double hydroxide (ZnAl-LDH) was functionalized with 2-phenylbenzimidazole-5-sulfonic acid (PBSA) to prepare ZnAl-PBSA-LDH using a simple one-step method. The electrochemical impedance spectroscopy (EIS) result of the solution phase demonstrated excellent corrosion inhibition performance of ZnAl-PBSA-LDH. Subsequently, 0.6 wt.% ZnAl-PBSA-LDH with shielding effects and active inhibition was incorporated into the water-based epoxy (WEP) for preparing the high-performance anti-corrosion coating (6-ZPL/WEP). The EIS test illustrated that the 6-ZPL/WEP coating maintained a high low-frequency impedance modulus (|Z0.01 Hz|) after 30 days of immersion, which is nearly two orders of magnitude higher compared to that of the blank coating. These results demonstrated that ZnAl-PBSA-LDH could efficiently improve the corrosion resistance of the WEP coating. Therefore, this study introduces new insights into the use of layered double hydroxides (LDHs) in the domain of anti-corrosion.