Octanoic acid was chosen as the biomass model for studying the catalytic hydrogenation reaction. The effect of support species and structure on catalytic activity was studied in this work. Ni nanoparticles supported on metal oxide supports (ZrO2, SiO2, Al2O3, and TiO2) were characterized and examined for their catalytic properties. Ni/ZrO2 exhibited high catalytic activity with 68.7% octanoic acid conversion owing to favorable hydrogen dissociation and spillover on Ni/ZrO2. Upon further study, Ni/ZrO2 with a three-dimensional ordered microporous structure (3DOM-ZrO2) and a hollow spherical structure (HS-ZrO2) has been prepared for octanoic acid catalytic hydrogenation. Compared to traditional structures, a catalyst with the 3DOM structure is beneficial for efficient contact of reactants and catalysts in heterogeneous catalysis. The reactant fluids efficiently contacted with the catalytic active center in the 3DOM structure catalyst promoting the catalytic activity, which was simulated by computational fluid dynamics (CFD).