Bio-oil from biomass pyrolysis is promising to be used as a sustainable biofuel and high-value-added chemical. However, the presence of high acid, water, and oxygenate causes corrosive properties, low higher heating value (HHV), and instability of the bio-oil component. Therefore, refining the bio-oil is essential to improve its quality. In this study, we introduced natural zeolite (HZ) impregnated with transition metal oxide (TMO) to refine the bio-oil using the hydrodeoxygenation method (HDO) at various catalyst ratios and temperatures. We find that ZnO/HZ 5% wt. shows the best catalytic performance, with the conversion of organic phase reaching ∼ 50%. The refined bio-oil from Fe2O3, ZnO, and CuO has high-quality physicochemical properties with carbon, oxygen, water level, and HHV values are 37–52%, 40–53%, 8–27%, and 17–21 MJ/kg, respectively. This result represents a high catalytic performance for the hydrodeoxygenation process of bio-oil using natural zeolite-based transition metal oxide for better and low-cost biofuel production.