Objective To investigate the clinicopathological characteristics, diagnosis and surgical treatment of multiple primary hypopharyngeal cancer and thoracic esophageal cancer. Methods Seven male patients with multiple primary hypopharyngeal cancer and thoracic esophageal cancer underwent surgical treatment during Jan. 2002 to Jan. 2008. Their clinical data, including the adjuvant examination method, clinical staging, pathological types, and operative methods, postoperative complications, and long-term outcomes, were retrospectively analyzed. Results Six patients were confirmed to have the disease before operation, and one patient was pathologically confirmed after operation. All patients had squamous cell carcinoma, with all the thoracic esophageal lesions and four hypopharyngeal lesions being well-differentiated, and three hypopharyngeal lesions being moderately differentiated. All cases underwent total laryngectomy, total hypopharyngectomy and total esophagectomy, and were reconstructed with gastropharyngostomy. There was no perioperative death and the swallowing function recovered satisfactorily after operation in all cases. One patient had postoperative pleural effusion and one had postoperative wound infection, which were cured after conservative treatment. All patients were followed up. One patient survived tumor-free for five years, two patients died two years after operation due to recurrence, and one died 10 months after operation due to local recurrence and bleeding. Conclusion Multiple primary hypopharyngeal cancer and thoracic esophageal cancer have similar characteristics, and various adjuvant examinations should be used routinely to avoid missed diagnosis. Total hypopharyngectomy and total esophagectomy combining reconstruction with gastropharyngostomy are easy to perform; they can be the first choice for the condition.