The invention provides a method for preparing an organic synergistic soil conditioner. The soil conditioner comprises the following components in portion by weight: 30 to 60 portions of organic component, 9 to 23 portions of synergistic component, 10 to 23 portions of conditioning component, and 15 to 30 portions of inorganic nutrient. The soil conditioner is prepared by the method of weighing, mixing, spray granulation and low-temperature drying, wherein the organic component contains 2 to 5 portions of humic acid, 25 to 45 portions of mature garbage or barnyard manure, and 2 to 5 portions of residue of monosodium glutamate and sugar production; the synergistic component contains 1 to 3 portions of zeolite powder, and 8 to 20 portions of synergistic agent; the conditioning component contains 2 to 10 portions of plaster, 9 to 13 portions of bentonite, 4 to 8 portions of polyvinyl alcohol (liquid), and 0.5 to 1.2 portions of starch (liquid); and the inorganic nutrient contains 4 to 7 portions of urea, 7 to 9 portions of ammonium phosphate, 5 to 7 portions of potassium sulfate, and 4 to 6 portions of ammonium sulfate. The preparation method is scientific, reasonable, simple and easy to operate; and the preparation method solves the synergistic effect of soil conditioners, and is suitable for the planting of field crops and forest fruits, in particular suitable for the conditioning of saline-alkali soil. By the determination of the national standard GB18877-2002, various indexes satisfy the national standard, and the content of the humic acid exceeds the standard requirement.