The invention belongs to a preparation method of polyester polyol of modified isocyanate, a preparation method of isocyanate prepolymer and a preparation method of polyurethane elastomer. The preparation method of the polyester polyol of the modified isocyanate comprises the following step of: reacting component A and component B at the temperature of between 60 and 80 DEG C under the protection of nitrogen, wherein the component A is one or more of polyester polyols which have 2 to 3 functionality degrees and the hydroxyl value which is between 50 and 500mgKOH/g; and the component B is modified isocyanate. The preparation method of the isocyanate prepolymer comprises the following step of: reacting the polyester polyol of the modified isocyanate and one or more of organic diisocyanates at the temperature of between 60 and 80 DEG C under the protection of nitrogen. The preparation method of the polyurethane microporous elastomer comprises the following step of: blending the modified isocyanate-containing polyester polyol, the isocyanate prepolymer and one or more of compounds selected from a chain extender, a catalyst, a foaming agent and a mixture of the chain extender, the catalyst and the foaming agent at the speed of between 5,000 and 7,000 revolutions per minute, wherein the index of the isocyanate is 100 percent.