To investigate the clinical effect of fenestration decompression in patients with oral and maxillofacial cysts. Methods A total of 50 patients with oral and maxillofacial cysts who underwent surgical treatment in our hospital from May to November 2023 were selected as the research objects. They were divided into control group and observation group according to different surgical schemes, with 25 patients in each group. The control group was treated with conventional incision, and the observation group was treated with fenestration decompression. The clinical indexes, clinical efficacy, treatment satisfaction and complications were compared between the two groups. Results The operation time, intraoperative blood loss and hospitalization time of the observation group were better than those of the control group (P <0.05). The total effective rate of treatment in the observation group was 96.00%, which was higher than 72.00% in the control group (P <0.05). The treatment satisfaction of the observation group was 96.00%, which was higher than 76.00% of the control group (P <0.05). The incidence of complications in the observation group was 4.00%, which was lower than 24.00% in the control group (P <0.05). Conclusion Fenestration decompression can effectively shorten the operation time and hospitalization time of patients with oral and maxillofacial cysts, and reduce the amount of intraoperative blood loss. Meanwhile, its treatment effect is better than that of conventional incision treatment, which is conducive to reducing the incidence of related complications and improving patient satisfaction.