The invention provides a method for comprehensively recovering tungsten and fluorine from minerals, namely a mixed acid of phosphoric acid and sulfuric acid is adopted for decomposing complex calcium-containing minerals containing fluorite, scheelite, apatite, and calcite, wherein the fluorite is decomposed to fluorine hydride or silicon tetrafluoride to escape, and absorption treatment is performed for preparing hydrofluoric acid or a fluoride salt; and the scheelite is transformed to phosphotungstic acid to enter into a solution, and filtrate after filtration is supplemented into the consumed sulfuric acid and the phosphoric acid after extraction of the tungsten and returned to the new-round mineral leaching. The method disclosed by the invention has the advantages of comprehensively recovering the fluorine and the tungsten from the minerals, reducing the requirements on the fluorite or the tungsten ore raw material, reducing the pressure on a mineral dressing link, improving the comprehensive recovery rate and simultaneously ensuring the decomposition rate of the fluorite and the scheelite, wherein the decomposition rate of the fluorite is above 98%, and WO3 contained in decomposition slag is reduced to below 0.5%; furthermore, a leaching agent can be recycled, so that leaching cost and wastewater emission are greatly reduced; and the method also has the advantages of simple leaching equipment, convenience in operation and easiness in realization of industrialization.