The invention relates to a preparation method and an application method of a tomato special fertilizer, wherein the preparation method comprises the following steps: preparing an I-type fertilizer by taking the following ingredients in parts by weight: 20-30 parts of urea, 20-30 parts ammonium phosphate, 15-20 parts of potassium sulphate, 1-3 parts of humic acid, 1-3 parts of rubbish and excrement, 1-5 parts of synergist, 0.1-1 part of ferrous sulphate, 0.1-0.8 part of zinc sulfate, 0.1-0.6 part of manganese sulphate, 0.1-0.6 part of borax, 0.1-0.4 part of copper sulfate, 2-7 parts of plaster and 3-13 parts of bentonite; preparing an II-type fertilizer by taking the following ingredients in parts by weight: 20-30 parts of urea, 5-10 parts ammonium phosphate, 35-45 parts of potassium sulphate, 1-3 parts of humic acid, 1-5 parts of rubbish and excrement, 2-5 parts of synergist, 0.1-1 part of ferrous sulphate, 0.1-0.8 part of zinc sulfate, 0.1-0.6 part of manganese sulphate, 0.1-0.6 part of borax, 0.1-0.4 part of copper sulfate, 2-7 parts of plaster and 3-13 parts of bentonite; evenly blending, spraying, pelleting, adding 1-6 parts of diluted polyaspartic acid, drying at lower temperature and detecting to be qualified to obtain the special fertilizer. The application method of the special fertilizer comprises the following steps: applying an organic fertilizer and the II-type fertilizer before spring sowing; applying the II-type fertilizer at the flowering and fruiting periods, and applying the II-type fertilizer in the young fruit development period; and the .production yield can be increased by 16-18 percent.