Objective To analyze the effect of fenestration decompression in patients with oral and maxillofacial bone cyst. Methods A total of 60 patients with oral and maxillofacial cysts admitted to our hospital from May 2022 to May 2023 were randomly divided into control group and observation group, with 30 patients in each group. The control group was treated with cyst curettage, and the study group was treated with fenestration decompression. The clinical efficacy, clincal indicator and scar disappearance rate were compared between the two groups. Results The total effective rate of treatment in the study group was 93.33%, which was higher than 70.00% in the control group (P <0.05). The operation time, intraoperative blood loss and hospitalization time of the study group were better than those of the control group (P <0.05). The rate of scar disappearance in the study group was higher than that in the control group (P <0.05). Conclusion The clinical effect of fenestration decompression in the treatment of oral and maxillofacial bone cysts is better than that of cyst curettage, which can improve the total effective rate of treatment, shorten the operation time and hospitalization time, reduce the intraoperative blood loss and promote the disappearance of scars.