The invention discloses an alternative split applicator for seed manure. The alternative split applicator for the seed manure comprises a fertilizer chamber cover, a seed chamber cover, a fertilizer taking device, a seed manure conveying wheel, a seed taking device, a shell and a rotating shaft. According to the alternative split applicator for the seed manure, the fertilizer taking device, the seed manure conveying wheel and the seed taking device rotate along with the rotating shaft by rotating the rotating shaft; a fertilizer in a fertilizer tank and seeds in a seed tank orderly and alternatively flow out from a discharging device; meanwhile, the alternative split applicator for the seed manure horizontally moves along the direction of the planting trench. Thus, the alternative split application effect of the seed manure is achieved. By adopting the alternative split applicator for the seed manure, the work efficiency is improved, the labor intensity is reduced, and the production cost is also reduced. Meanwhile, the invention also discloses an alternative split application method for the seed manure of the alternative split applicator for the seed manure.