The invention discloses a biodiesel hydrodeoxygenation process which is characterized by comprising a fixed bed reactor filled with hydrodeoxygenation catalysts, the catalysts include carriers, active components and catalytic auxiliaries, the carriers are KIT-1 with synthetic skeleton structures doped with heteroatoms Co2+, the active components are molybdous nitride MO2N, tungsten nitride W2N, molybdenum carbide Mo2C and tungsten carbide WC mixture, and the catalytic auxiliaries are TiO2, CeO2, V2O5 and NbOPO4 mixture. The reaction condition of the fixed bed reactor includes reaction temperature of 300-450 DEG C, hydrogen pressure of 2.5-3.5MPa, hydrogen to oil volume ratio of 500-800, and volume space velocity of 1.0-2.5h<1>. By the process, the hydrodeoxygenation rate of biodiesel can be controlled to be high (99.8% or more), and catalytic activity cannot be obviously reduced in continuous running for 500 hours.