The invention relates to a method for preparing noncrystalline polyester polyol which is used for preparing hot setting adhesive. The method comprises the steps as follows: materials of terephthalic acid, phthalic acid or m-phthalic acid, hexane diacid, glycol, neopentyl glycol and nonmetallic catalyst are put into a polymerizing pot at a time to be heated up and dehydrated while keeping the temperature; after the temperature rises to 220-230 DEG C, the temperature is kept, and acid value is measured; when the acid value of the materials is lower than 15mgKOH/g, the materials are vacuumized; when the acid value is less than or equal to 2mgKOH/g, and hydroxyl value is 30-200mgKOH/g, the materials are cooled and discharged, and the noncrystalline polyester polyol is obtained. The preparation method has simple process and is protective to the environment. The prepared noncrystalline polyester polyol belongs to a polylol soft segment structure with relatively random main chain and achieves the noncrystalline effect. Moisture cured polyurethane adhesive prepared by the noncrystalline polyester polyol has good mechanical adhesive performance, so that the developing time is prolonged, and the finial strength is close to 9MPa.