In this study, we prepared a novel coating composed of hexagonal molybdenum oxide (h-MoO3) nanofiller and waterborne epoxy resin (WEP) to provide corrosion protection. We optimized the h-MoO3 nanorod synthesis methodology first by changing different parameters (pH, temperature, etc.). Furthermore, the as-prepared h-MoO3 rods were characterized using a scanning electron microscope (SEM) and X-ray diffraction (XRD). Finally, the electrochemical impedance spectroscopy (EIS) test results verified that the anticorrosive performance of the composite coatings was improved by incorporation of low content of MoO3 nanofiller (0.5 wt.%) compared to pure WEP sample. This developed composite will provide a new insight for the design and fabrication of one-dimensional (1D) nanomaterial (e.g., nanorod) reinforced epoxy coating and other polymeric coating processes.