The invention discloses a multifunctional acid soil conditioner and an application method thereof. The multifunctional acid soil conditioner is prepared by mixing 10 to 25 percent of magnesium hydroxide, 15 to 30 percent of calcium carbonate, 5 to 25 percent of calcium hydroxide, 10 to 25 percent of calcium magnesium phosphate fertilizer, 0 to 15 percent of lime nitrogen, 0 to 30 percent of lignite, 0 to 30 percent of danty, 0 to 30 percent of peat, 0 to 2 percent of borax and 0 to 3 percent of zinc sulfate in percentage by weight, and stirring uniformly. For solving the series of problems that southern soil is serious in acidification, degenerate in structure and frequent in soil-borne disease, on the basis of combining a great amount of field trial results, an acid soil conditioner formula having the functions of providing nutrition, improving the soil, killing the soil-borne disease and the like is developed, and meanwhile a certain amount of medium trace elements and synergists are added in the formula, so that the formula can meet the need of plants on medium trace nutrient elements in a growth development process, so as to remarkably improve the yield and quality of crops.