Hydrodeoxygenation (HDO) of two dilute acid flow through pretreated softwood lignin samples, including residual lignin in pretreated solid residues (ReL) and recovered insoluble lignin in pretreated liquid (RISL), with apparent different physical and chemical structures, was comprehensively studied. A combination of catalysts (HY zeolite and Ru/Al<
sub>
2<
/sub>
O<
sub>
3<
/sub>
) was employed to investigate the effects of lignin structures, especially condensed structures, on the HDO upgrading process. Results indicated that the condensed structure and short side chains in lignin hindered its HDO conversion under different reaction conditions, including catalyst loading and composition, hydrogen pressure, and reaction time. In addition to lignin structure, HY zeolite was found crucial for lignin depolymerization, while Ru/Al<
sub>
2<
/sub>
O<
sub>
3<
/sub>
and relatively high hydrogen pressure (4 MPa) were necessary for upgrading unstable oxy-compounds to cyclohexanes at high selectivity (>
95 wt %). Since the lignin structure essentially affects its reactivity during HDO conversion, the yield and selectivity of HDO products can be predicted by detailed characterization of the lignin structure. Furthermore, the insights gained from this study in the fundamental reaction mechanisms based on the lignin structure will facilitate upgrading of lignin to high-value products for applications in the production of both fuels and chemicals.