In this study, novel nickel-molybdenum nanoparticles catalysts stabilized with ether-functionalized ionic polymer (Ni-Mo NPs@IP) were successfully synthesized and characterized by X-ray diffraction method (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analysis. The prepared nanocatalyst was examined in the aqueous phase catalytic hydrodeoxygenation of anisole (a model compound) on a batch reactor at 80–200 °C and 10–50 bar. The catalytic upgrading of anisole in the presence of different ratios of Ni-Mo NPs@IP includes the following: anisole conversion to phenol by hydrogenolysis, to benzene by hydrodeoxygenation, and to cyclohexane by hydrogenation. The experimental results demonstrated that the catalytic activity of Ni-Mo (50%–50%) nanoparticles stabilized with IP is superior to that with low Mo content and that raising the Mo loading by more than 50% has no discernible effect on anisole conversion. Furthermore, the results indicated that oxygen removal could be a desirable phenomenon by operating at higher temperatures, pressures, and reaction times. Furthermore, the catalytic tests under different operating conditions have indicated the superior activities of Ni-Mo NPs@IP in converting a phenolic compound into de-oxygenated fuel-grade products. The sensitivity analysis of operating condition reveals that the maximum HDO conversion is achieved over Ni-Mo (20%–80%) NPs@IP at temperature of 200 °C, hydrogen pressure of 50 bar, reaction time of 15 h and catalyst loading of 5 mol%.