The invention discloses an industrial production method of 2-methylthio-4,6-difluoropyrimidine. 2-methylthio-4,6-dichloropyrimidine and potassium fluoride are taken as raw materials, sulfolane is taken as a solvent, the materials have a high-temperature substitution reaction, and 2-methylthio-4,6-difluoropyrimidine is generated; large quantity of inorganic salts is removed through hot centrifugation, and a finished high-content 2-methylthio-4,6-difluoropyrimidine product is separated out with a steam distillation method. Water and the solvent sulfolane can be recycled from bottom residues after product separation respectively through reduced pressure distillation. According to the process, the product yield is higher than 85%, the product content is higher than 98%, and the water content is lower than 0.2%. The production process is pollution-free and green, the yield is high, reduction of the production cost is facilitated, the product purity is high, and later application is facilitated.