The invention relates to the technical field of recycling of industrial waste residues and discloses a method for preparing silicon fertilizers by using industrial waste residues. The preparation method comprises the following steps: adding electrolytic manganese residues, fly ash, sodium carbonate and sodium hydroxide in a planetary ball mill, ball-milling for 20-60 minutes at a rotating speed of 150-250 r/min according to the ball-material ratio of 5-10 g/g, uniformly mixing, then putting in a microwave high-temperature sintering furnace, controlling the temperature within 750-850 DEG C, calcining for 10-60 minutes and crushing to prepare the silicon fertilizers based on the industrial waste residues. The silicon fertilizers reach NY/T797-2004 silicon fertilizer standard of the Ministry of Agriculture of the People's Republic of China. The method disclosed by the invention has the benefits that a large quantity of electrolytic manganese residues can be effectively utilized, the production process is short, the operation is convenient, wastes are changed into valuables, and an effective way is provided for the resource utilization of the manganese residues.