To develop an efficient catalyst for deoxygenation (DO) as the first step in biojet fuel production with silica-supported Ni/Al catalysts, the effects of silica supports were investigated in terms of pore structure, acidity, and pore size. The pore structures of silica were covered from microporous SiO2 to mesoporous SBA-15, SBA-16, and KIT-6. Then, taking a simple tubular structure of Ni/Al-SBA-15 with the best biojet fuel yield, samples with various acidity and pore sizes were further prepared through manipulation of the amount of aluminum (Al)-incorporation and the temperature of hydrothermal synthesis, respectively. The DO reactivity of the prepared silica-supported Ni/Al catalysts was assessed with methyl palmitate as a model compound of biomass feedstock. Based on the altered physicochemical properties of not only the silica support but also the supported Ni, the relationship between the variation of silica supports and their DO catalytic properties was investigated. This work provides a better understanding of silicasupported Ni/Al catalysts and how to design selective catalysts for DO reaction to maximize the biojet fuel hydrocarbon yield.