SBA-15 supports with incorporated Zr and/or Ce were synthesized using direct hydrothermal synthesis, followed by ammonia evaporation to prepare Ni–phyllosilicate-derived catalysts. The effect of zirconium and cerium ions present in the silica framework in catalyzing the high-temperature water–gas shift (WGS) reaction and circumventing the undesired methanation reaction was investigated over the temperature range from 250 to 500 °C. Diffuse-reflectance infrared Fourier transform spectroscopy revealed that surface hydroxyl species on silica were involved in promoting WGS activity for all catalysts. Furthermore, the presence of Zr and Ce in the silica framework could minimize the formation of Ni subcarbonyl species and enhance the adsorption of CO on Ni. At 375 °C, the Ni/Zr–Ce-SBA-15 catalyst achieved excellent catalytic activity in the WGS reaction in terms of turnover frequency (4.57 s−1) and hydrogen formation rate (534 μ mol H2 g−1s−1). A dual-site carboxyl mechanism was proposed to be the plausible pathway over the Ni/Zr–Ce-SBA-15 catalyst.