Objective To summarize the clinical characteristics of patients with branchial cleft anomalies and to discuss the diagnostic and treatment options.Methods Clinical data of 87 patients diagnosed with branchial cleft anomalies from January 2000 to September 2022 were collected and analyzed retrospectively in the light of the literature.Results In this group, 10 patients had first branchial cleft deformity, 52 had second branchial cleft deformity, 20 had third branchial cleft deformity and 5 had fourth branchial cleft deformity. Fifteen patients had previous history of relevant neck surgery. All patients were treated surgically, and only 1 case had temporary facial nerve paralysis, which recovered 3 months after surgery. Of all the 87 patients, 81 completed postoperative follow-up ranging from 6 months to 16 years. Six patients had recurrence after surgery, and were treated again in our hospital with cervical mass resection plus plasma piriform fossa fistula closure without recurrence during 7-8 years of follow-up.Conclusions The diagnosis of congenital branchial cleft anomaly is difficult and this disease is relatively easy to recur. The preoperative combination of various examinations can improve the diagnostic accuracy, and complete surgical excision of the lesion is the preferred treatment option. In patients with acute infection, cervical debridement should be performed first, and then surgical resection can be carried out in stable period to reduce the recurrence rate.