Primary adenoid cystic carcinoma (ACC) of the trachea with thyroid invasion is very rare. In this report, we present a 46-year-old man with primary ACC of the trachea with thyroid invasion. ACC invasion of the thyroid is very rare and is easily misdiagnosed. The patient sought consultation due to a 6-month history of dysphagia and associated dyspnea. A contrast-enhanced computed tomography scan obtained at the time of admission revealed bilateral thyroid masses and tracheal wall thickening. The thyroid masses were fused to the trachea and the esophagus without discernible borders, intraoperatively. Frozen pathology suggested poorly differentiated cancer, and a bilateral partial thyroidectomy was performed. Postoperative pathology revealed primary tracheal ACC with thyroid invasion. The patient died 1 month after surgery. We have also summarized the literature on the clinical presentation, diagnosis, and treatment of thyroid-invasive ACC.