The invention discloses a special sesame hydroponic nutrient solution and a preparation method thereof. The special sesame hydroponic nutrient solution consists of the following components (by every 1000ml): 80-200mg of urea, 10-30mg of monopotassium phosphate, 50-70mg of potassium chloride, 30-50mg of magnesium sulfate, 1-3mg of zinc sulfate, 2-5mg of copper chloride, 3-5mg of ferrous sulfate, 1-2mg of manganese sulfate, 1-3mg of calcium chloride, 2-3mg of borax, 0.01-0.03mg of sodium molybdate, 1-3ml of a rare-earth nutrient solution and the balance of water. The special sesame hydroponic nutrient solution disclosed by the invention is scientific in formula and moderate in proportion, disease resistance of sesames can be improved, and diseases (blight, damping off and root rot) in a sesame seedling period can be effectively prevented. The nutrient solution comprises all nutrition elements essential for sesame to grow, is balance in nutrition, green and environmental-friendly, low in cost, applicable to sesame and crops such as pasture and green manure which need a relatively small amount of fertilizers in growth periods as well. The special sesame hydroponic nutrient solution is simple in raw material source, free of harmful substance, free of environment pollution and harmless to human beings or livestock.