Objective There is considerable evidence linking gut microbiome to bone-joint diseases, but no studies explored the causal association between gut microbiome and carpal tunnel syndrome (CTS).Methods This study utilized large-scale genome-wide association studies (GWAS) summary statistics to evaluate the causal association between gut microbiome and CTS. Two-sample Mendelian randomization (MR) approach was used to identify the causal microbial taxa for CTS. Comprehensively sensitivity analysis was performed to validate the robustness of results. Reverse-direction MR analysis was performed to rule out the possibility of reverse associations.Results Multiplicative random effect inverse variance weighted (IVW_mre) method suggested that 4 gut microbial taxa had a positive effect on CTS such as Actinobacteria (OR = 1.12, PIVW = 0.05) and Oxalobacter (OR = 1.06, PIVW < 0.01); 11 gut microbial taxa had a negative effect on CTS such as Methanobacteria (OR = 0.95, PIVW = 0.01), Rikenellaceae (OR = 0.92, PIVW = 0.03), Blautia (OR = 0.92, PIVW = 0.02), Butyrivibrio (OR = 0.94, PIVW = 0.01) and Lachnospira (OR = 0.86, PIVW < 0.01). Sensitivity analysis excluded the influence of heterogeneity and horizontal pleiotropy. According to the results of reverse-direction MR analysis, no significant causal effect of CTS was found on 15 gut microbial taxa.Conclusions Our study identified the causal relationships between several gut microbiomes and CTS. These findings may give insights into the mechanism of CTS and provide novel therapeutic targets.