Objective: To explore the diagnosis and treatment of ductal malformations of the submandibular gland with multiple stones. Methods: A case of a malformation of Wharton′s duct with multiple sialoliths according to the clinical data, diagnosis and treatment of the patient was analyzed retrospectively. Results: The patient′s physical examination and CBCT showed a tumor on the left floor of the mouth. In this case, it was found that the mass was a malformation of Wharton′s duct with multiple sialoliths according to operative exploration. The postoperative pathological examination showed (left submaxillary) salivation gland tissue, duct dilation and duct epithelia hyperplasia, duct calculus, and a large number of lymphocytes proliferating around the duct; 1 month after the follow-up, the patient had healed well. Through literature review and analysis, it was found that cases of submandibular ductal malformation with multiple stones were rare and should be carefully differentiated from arteriovenous malformation at the base of the mouth. Calculi of the submandibular gland can be removed by incision through the oral submandibular duct or by combined resection of the submandibular gland and ductal calculi, and some smaller calculi can also be treated by endoscopy of the salivary gland. Conclusion In cases of submandibular ductal malformation with multiple stones, intraoral and extraoral incisions should be performed simultaneously to remove the associated ductal stones.