Objective This study aims to evaluate the therapeutic effects of negative pressure suction drainage in treatment of odontogenic keratotic cystoma in the mandible. Methods Thirty-six patients with large odontogenic keratotic cystoma in the mandible were enrolled into the study. The patients were randomly divided into two groups and treated with negative pressure suction drainage and decompression by fenestration, respectively. The therapeutic effects were recorded and compared. Results The therapeutic effect of negative pressure suction drainage was better than that of decompression by fenestration. A significant difference was observed between the two groups. Conclusion Treating large odontogenic keratotic cystoma in the mandible with negative pressure suction drainage can reduce complications, has good effect in reducing and eliminating the cyst cavity, and has good effect in correcting maxillofacial deformities caused by bony expansion. Therefore, this method is worthy of clinical application.