The invention discloses a functional nutrition fertilizer, which comprises the following raw materials in parts by weight: 200-500 parts of organic wastes, 20-60 parts of grass carbon, 60-120 parts of livestock manure, 200-600 parts of rice washing water, 50-100 parts of seaweed mud, 10-50 parts of EM bacteria agent, 1-3 parts of ferrous sulfate, 1-3 parts of copper sulfate, 1-3 parts of zinc sulfate, 0.5-2 parts of manganese sulfate, 0.5-3 parts of ammonium molybdate, 0.3-2 parts of sodium tetraborate, 0.3-3 parts of strontium nitrate, 0.5-1 parts of selenium dioxide, 2-6 parts of magnesium sulfate, 3-8 parts of potassium chloride, 2-8 parts of calcium carbonate, 3-10 parts of bentonite, 5-10 parts of urea, 10-50 parts of traditional Chinese medicine extract, and 10-30 parts of traditional Chinese medicine residue fermented product. According to the functional nutrition fertilizer, the nutrition components are complete and balanced, the disease and insect resistance capacity of soil can be enhanced, the fertilizer efficiency of soil can be increased, and the functional nutrition fertilizer has no environment pollution. The invention further discloses a preparation method of the functional nutrition fertilizer.