Abstract The gut microbiota is closely related to the occurrence and development of cancer. However, the characteristics of gut microbiota associated with ovarian tumors remain elusive. In this study, fecal samples were collected from healthy control (HC) group and patients with ovarian tumor (OT) or with other benign tumor (OBT) for 16s rRNA sequencing to determine differential flora in gut microbiota. The composition of gut microbiota in the OT group, including bacterial abundance and diversity, was significantly different form HC and OBT groups. In the OT group, Escherichia_Shigella was markedly higher than in the HC group, while Coprococcus, Fusicatenibacter, Butyricicoccus and Oscillibacter were significantly lower than in HCs. The abundance of Fusicatenibacter, Butyricicoccus, Coprococcus Parasutterella, and Anaerotruncus in the OBT group was distinctly higher than that in the OT group, while the Lachnospiracae_ND3007_group was significantly lower. In addition, in OT patients, ovarian cancer (OC) and benign ovarian tumor (BOT) patients also showed a unique composition of gut microbiota. The random forest model was designed using different bacteria. Compared with HCs, area under curve (AUC) values for BOT and OC groups were 0.77 and 0.86, respectively. These findings suggest that some gut microbiota such as Escherichia_Shigella show a certain ability to distinguish between healthy individuals and patients with OT.