The hierarchical HZSM-5 zeolite was prepared successfully by a simple NaOH treatment method. The concentration of NaOH solution was carefully tuned to optimal the zeolite acidity and pore structure. Under NaOH treatment conditions, a large number of mesopores, which interconnected with the retained micropores, were created to facilitate mass transfer performance. There are very good correlations between the decline of the relative zeolite crystallinity and the loss of micropores volume. The Ni nanoclusters were uniformly confined in the mesopores of hierarchical HZSM-5 by the excessive impregnation method. The direct deoxygenation in N2 and hydrodeoxygenation in H2 of the methyl laurate were compared respectively over the Ni/HZSM-5 catalysts. In the N2 atmosphere, the deoxygenation rate of the methyl laurate on the Ni/HZSM-5 catalyst is relatively slow. In the presence of H2, the synergistic effect between the hydrogenation function of the metal and the acid function of the zeolite supports can make the deoxygenation level more obvious. The yield of hydrocarbon products gradually reached the maximum with the appropriate treatment concentration of 1M NaOH, which could be attributed to the improved mass transfer in the hierarchical HZSM-5 supports.