ObjectiveInvestigating the causal connection that exists between inflammatory bowel disease (IBD) and hypertension (HT). To gain a deeper insight into the correlation among IBD, gut microbiota, and HT, we conducted a two-step, two-sample Mendelian randomization study.MethodsAn investigation of genome-wide association study (GWAS) summary-level data was utilized to conduct a two-sample Mendelian randomization (MR) analysis of genetically predicted inflammatory bowel disease: (12,882cases, 21,770controls) on Systolic/Diastolic blood pressure (N = 2,564). Subsequently, two-step MR analyses revealed that the relationship between IBD and SBP was partly mediated by Faecalicatena glycyrrhizinilyticum. The robustness of the findings was confirmed through several sensitivity assessments.ResultsThis MR study showed that increase in genetically predicted IBD was associated with higher risk of genetically predicted SBP (OR: 1.08, 95% CI: 1.01–1.16, P < 0.05) and DBP (OR: 1.09, 95% CI: 1.02–1.17, P < 0.05), respectively. Inverse variance weighted (IVW) MR analysis also showed that increase in genetically predicted IBD was associated with higher abundance Faecalicatena glycyrrhizinilyticum (OR: 1.03, 95% CI: 1.01–1.04, P < 0.05), which subsequently associated with increased SBP risk (OR: 1.42, 95% CI: 1.06–1.9, P < 0.05). Faecalicatena glycyrrhizinilyticum abundance in stool was responsible for mediating 11% of the genetically predicted IBD on SBP.ConclusionThe research proposed a causal link between Inflammatory Bowel Disease (IBD) and Hypertension (HT), with a little percentage of the impact being influenced by Faecalicatena glycyrrhizinilyticum in stool. Mitigating gut microbiome may decrease the heightened risk of hypertension in people with inflammatory bowel disease.