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Gut microbiota with fecal metabolites play a role in mice with endometriosis. The gut microbiota disorder, such as abnormal abundance of Allobaculum, Akkermansia, Parasutterella, and Blautia, existes in intestine of mice with endometriosis (EMS), which can influence fecal metabolites and intestinal barrier. The increased abundance of chenodeoxycholic acid (CDCA) and ursodeoxycholic acid (UDCA) can enhance intestinal barrier and reduce inflammatory factors leakage, while the decreased abundance of alpha-linolenic acid (ALA) and 12,13s-epoxy-9z,11,15z-octadecaterienoic acid (12,13-EOTrE) may contribute to promoting inflammation and EMS lesions growth. CDCA can be converted into UDCA by the metabolism of gut microbiota.