The invention relates to the field of soil fertilizer and provides a biological organic repairing agent for soil pollution and its application and preparation method. The biological organic repairing agent of the invention is composed of, by weight, 1.5-3 parts of eymogenic bacterium, 1-1.5 parts of wheat bran, 1.5-2 parts of molasses meal, 45-50 parts of ammonium humate, 45-50 parts of hydrolase dregs, 150-200 parts of soybean meal, 100-150 parts of humic acid powder, 80-100 parts of zeolite powder, 25-40 parts of a calcium magnesium phosphate fertilizer, 150-200 parts of cattle and sheep manure, 150-204 parts of plant straw, 25-40 parts of potassium humate, 1.5-3 parts of bacillus mucilaginosus, 1-1.5 parts of Gliocladium roseum, 1.5-2 parts of Streptomycesvinaceus-drappus, 1-1.5 parts of trichoderma spp, 1-1.5 parts of Paecilomyces lilacinus, 1-1.5 parts of bacillus subtilis and 1-1.5 parts of micrococcus. According to the invention, soil pollution control, improvement and nutrition are integrated.