Abstract: Objective To compare the clinical effects of maxillary ostium with fenestration of lower nasal mucosal flap in treating maxillary sinus mucosa cyst. Methods We retrospectively analyzed the medical records of 63 patients with maxillary sinus mucosal cysts from July 2014 to July 2016. They were divided into two groups to be treated by fenestration of the lower nasal mucosa flap and the maxillary ostium. The operative time, intraoperative blood loss, postoperative in-hospital stay, surgical complications, and operative efficacy were compared between the two groups. T-test and Chi-square test were employed for data analysis. Results There was no significant difference in operation time, intraoperative blood loss, postoperative in-hospital stay, operative complications and surgical outcome (P>0.05) . Swelling in the inferior turbinate mucosa occurred in 2 cases treated by fenestration of the lower nasal mucosa flap, and lesion occurred in 1 case treated with maxillary ostium group (repeated surgery) .Conclusion Fenestration of the lower nasal mucosa flap had wider range of application than maxillary ostium. The treatment of maxillary sinus mucosal cysts should choose a reasonable surgical path.