The present method for allocating the nutrient of livestock manure from the scale raising farms is simply allocating the total amount of statistical data of scale raising farms according to the area of farmland taking administration cell as unit. In this method, it is thought that there are no differences among the farmlands and the amount of statistical data of scale raising farms is only closely related to the area of farmland in a administration cell. The specialization algorithm of statistical data of scale raising farms was constructed based on the spatial differences among the farmlands and the particularity of livestock manure from the scale raising farms, when it applied as the fertilizer to farmland using theory and technique of GIS spatial analysis. With the maximum nutrient load of farmland, the statistical data of scale raising farms were transformed to the supply of regional nutrient of livestock manure. Finally, the specialization algorithm was carried out at the town of Shangjie to realize the application. The results of practical application show that the maximum values of nitrogen and phosphorus load of farmland were 169994kg/hm2 and 34973kg/hm2,which both were below the threshold value of 170kg/hm2 and 35kg/hm2 respectively. And it also shows that the method could reflect the spatial differences between the farmlands and was closer to the practical results of livestock manure than the present method.