Bio-oil from biomass pyrolysis cannot directly substitute traditional fuel due to compositional deficiencies. Catalytic hydrodeoxygenation (HDO) is the critical and efficient step to upgrade crude bio-oil to high-quality bio-jet fuel by lowering the oxygen content and increasing the heating value. However, the hydrocracking reaction tends to reduce the liquid yield and increase the gas yield, causing carbon loss and producing hydrocarbons with a short carbon-chain. To obtain high-yield bio-jet fuel, the elucidation of the conversion process of biomass catalytic HDO is important in providing guidance for metal catalyst design and optimization of reaction conditions. Considering the complexity of crude bio-oil, this review aimed to investigate the catalytic HDO pathways with model compounds that present typical bio-oil components. First, it provided a comprehensive summary of the impact of physical and electronic structures of both noble and non-noble metals that include monometallic and bimetallic supported catalysts on regulating the conversion pathways and resulting product selectivity. The subsequent first principle calculations further corroborated reaction pathways of model compounds in atom-level on different catalyst surfaces with the experiments above and illustrated the favored C–O/C=O scission orders thermodynamically and kinetically. Then, it discussed hydrogenation effects of different H-donors (such as hydrogen and methane) and catalysts deactivation for economical and industrial consideration. Based on the descriptions above and recent researches, it also elaborated on catalytic HDO of biomass and bio-oil with multi-functional catalysts. Finally, it presented the challenges and future prospective of biomass catalytic HDO.