Hierarchical ZSM-5 catalysts were prepared by desilication with different NaOH concentrations. Their structure and acidity were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), N-2 adsorption and desorption, ammonia temperature-programmed desorption (NH3-TPD), pyridine Fourier transform infrared (FTIR) spectroscopy, CO chemisorptions, and hydrogen temperature-programmed desorption (H-2-TPR). The catalytic conversion of jatropha oil into alternative fuel over the NiMo/hierarchical ZSM-5 catalysts was investigated. The deoxygenation pathways were tuned by controlling the alkaline treatment. The DCO2 reaction was strongly favored by strengthening the support-active phase interaction. The aromatization reaction among C2C8 olefins led to the increase of organic liquid products, especially the C9C15 hydrocarbons. In addition, this reaction was significantly improved by partial amorphization of the support but inhibited by the development of intracrystal mesopores. The larger mesoporous structure improved the selectivity of C9C15 paraffins. Moreover, the intracrystal mesopores had better catalytic cracking selectivity for C9C15 paraffins than pure microporous structure and amorphous structure.