Molybdophosphoric (HPMo) and tungstophosphoric (HPW) acid catalysts, supported on hexagonal mesoporous silica (HMS) carriers and modified with Ti, Zr, and Zr + Al, were prepared. The catalysts were characterized by Fourier transform IR spectroscopy of adsorbed pyridine and deuterated acetonitrile, X-ray photoelectron spectroscopy, and 31P and 1H nuclear magnetic resonance. Catalytic activity was tested in the hydrodesulfurization reaction of DBT. The thermal stability and the properties of the supported molybdophosphates and tungstophosphates were discussed in terms of support effect. For the hydrodesulfurization reaction, which was carried out under high hydrogen pressure, the HPMo/ZrAlHMS catalyst had higher activity and selectivity to biphenyl formation than the other supported HPMo catalysts. Regardless of the carrier, supported HPW catalysts were the most active.