The invention discloses a method of preparing highly pure silicon dioxide from silicon slag. The method comprises following steps: step one, adding a sodium hydroxide solution into organic silicon slurry to dissolve organic silicon, and filtering the solution to obtain a sodium metasilicate solution; step two, adding the sodium metasilicate solution prepared in the step one into a sodium carbonatesolution, introducing CO2 into the solution to carry out carbonization decomposition, and after reactions, carrying out solid-liquid separation to obtain metasilicic acid precipitates and sodium carbonate precipitates; and step three, washing the metasilicic acid precipitates prepared in the step two by acid and water, and drying the precipitates to obtain highly pure silicon dioxide. The waste namely organic silicon slurry, which is generated during the organic silicon production process, is taken as the raw material to produce highly pure silicon dioxide, the wastes are utilized, and the method is economic and environmentally-friendly.