The invention relates to a silicon-containing distillate oil hydrofining method, which adopts the method that the silicon-containing distillate oil raw material and hydrogen pass through at least two hydrofining catalyst beds under the hydrofining condition, the silicon-containing distillate oil raw material first passes through a hydrogenising catalyst bed with the silicon catching function, and then passes through a conventional hydrofining catalyst bed; wherein the hydrogenising catalyst with the silicon catching function has a greater pore volume and a specific surface area and a relatively lower metal content. Compared with the prior art, the method has the advantages that the process is simple, the good hydrodesulfurization and hydrodedenitrification performance is kept on the premise of enhancing the silicon-containing ability, and the running period of the device is effectively prolonged. The method can be applied to various silicon-containing distillate oil hydrofining processes.