Gut microbiota transplantation has been reported to improve the renal function of membranous nephropathy (MN). However, whether there is a causal effect of gut microbiota on MN remained unclear. We performed two-sample Mendelian randomization (MR) analysis. The inverse variance weighted (IVW) method was used as the main approach to evaluate the causal relationship between gut microbiota and MN. Additional methods including MR-Egger regression, weighted median, and MR-weighted mode were also conducted. Cochrane’s Q test, MR-Egger regression, and MR-PRESSO were employed to detect heterogeneity and pleiotropy, respectively. A total of 196 gut microbiota were examined. After IVW and sensitivity analysis, eight gut bacteria taxa were observed causal effects on the risk of MN. Specifically, Genus. Oscillibacter was a protective factor (OR: 0.57; 95%CI: 0.328-0.979; P = 0.042), while Class. Melainabacteria (OR: 1.51; 95% CI: 1.004-2.277; P = 0.048), Genus. Butyricicoccus (OR: 2.16; 95% CI: 1.005-4.621; P = 0.048), Genus. Catenibacterium (OR: 1.49; 95% CI: 1.043-2.134; P = 0.028), Genus.Ruminiclostridium5 (OR: 1.74; 95% CI: 1.053-2.862; P = 0.030), Genus. Ruminococcaceae UCG-003 (OR: 1.73; 95% CI: 1.110-2.692; P = 0.015), Order. Bacillales (OR: 1.52; 95% CI:1.135-2.025; P = 0.0048) and Order. Gastranaerophilales (OR: 1.45; 95% CI: 1.010-2.085; P = 0.044) were risk factors. Heterogeneity was not significant for most single-nucleotide polymorphisms, and no statistical difference in pleiotropy. This study first indicated the causal association between specific gut microbiota and MN, which would be of great significance to guide clinical prevention and treatment in MN.