The invention provides a chain-limited dicarboxylic end capping agent, a preparation method and an application thereof in nylon elastomer. The structural expression of the chain-limited dicarboxylic acid end capping agent is: where X represents alkyl, cycloalkyl or aralkyl between NCO groups at both ends of diisocyanate. The preparation method of the end capping agent comprises the following steps: 2-amino-4-hydroxyl-6-methylpyrimidine reacts with diisocyanate in inert gas atmosphere to obtain product a; the product a is reacted with 3, 5-bis (methoxycarbonyl) benzoic acid activated by thionylchloride in an inert gas atmosphere to obtain a product b; the product b is reacted with sodium hydroxide in the presence of solvent to prepare chain-limited dicarboxylic acid. The nylon elastomer prepared by the invention contains urea pyrimidine ketone structure, which can form quadruple hydrogen bonds, and the nylon elastomer forms corresponding dimers due to the acting force of the hydrogen bonds, thus developing corresponding applications on self-repairing materials.