The invention relates to the technical field of biological medicine, and in particular, relates to an application of an anti-NMDAR autoantibody as a congenital megacolon diagnostic marker. It is found that the anti-NMDAR autoantibody has the advantages of being easy to operate, free of intervention, high in flux and low in cost in children congenital disease diagnosis, and the defect that plasma diagnosis is not available in the prior art is overcome. The method has good diagnosis sensitivity and specificity, the AUC value is 0.9046, the optimal limit corresponding sensitivity is 93.75%, and the specificity is 81.58%. Besides, children suffering from the congenital megacolon are represented as vomiting, abdominal distension, constipation, enteritis and the like, the children suffering from the symptoms are large, the children suffering from the congenital megacolon account for a small amount, and a simple and effective screening method is needed. When the method is used for disease screening, the sensitivity is 100%, the specificity is 78.95, and the method can be used for disease screening.