The study used two-sample Mendelian randomization (MR) to investigate the effect of gut microbiota on functional dyspepsia (FD) through plasma metabolites, followed by experimental validation in rats. Genetic tools were created from GWAS data of 7,738 people for 412 microflora traits, 1,400 metabolites from the NHGRI-EBI catalog and FD data from the FinnGen biobank. Using the IVW method, causal relationships were established, confirmed by pleiotropy and heterogeneity tests. Protective factors against FD were pyridoxal 5′-phosphate biosynthesis superpathway (OR: 0.89; 95% CI: 0.81–0.97; p=0.01), pActinobacteria (OR: 0.85; 95% CI: 0.77–0.94; p=0.002) and sBifidobacterium (OR: 0.75–0.97; p=0.002). p=0.017). Risk factors included menaquinol-8 biosynthesis superpathway II (OR: 1.13; 95% CI: 1.03–1.25; p=0.01) and sLachnospiraceae bacterium5163FAA (OR: 1.09; 95% CI: 1.02–1.16; p=0.008). These three taxa and two pathways affect FD by regulating 81 plasma metabolites or their ratios. An experiment on rats (model with 0.2% iodoacetamide and stress) confirmed changes in pActinobacteria, alpha-hydroxyisocaproate and kynurenate.