The invention discloses a method of recovering nickel, iron and silicon from limonite by a combined leaching process, relates to a hydrometallurgical process of limonite, and particularly relates to a method of subjecting high-silicon high-magnesium ore of the limonite to sulfuric acid atmospheric-pressure leaching and subjecting low-silicon low-magnesium high-iron components to pressure leaching by utilization of atmospheric-pressure leachate in a same process so as to recover nickel (cobalt) and to economically and effectively recover iron that is the main component of ore and a part of silicon simultaneously. The method achieves efficient development and utilization of the limonite, adopts the process combining the atmospheric-pressure acid leaching and the medium-pressure leaching, overcomes the defects that present high-pressure acid leaching processes need autoclaves and related devices so that manufacturing and maintenance costs are high, and overcomes the technical problem that the high-pressure acid leaching processes are high in acid consumption and are limited to treatment of limonite type raw materials. Compared with atmospheric-pressure leaching processes, the method has beneficial effects comprising higher nickel and cobalt recovery rates, easy and effective separation of leached slag, and the like.