BackgroundThe gut microbiota has been significantly associated with differentiated thyroid cancer (DTC). However, the causal relationship between the gut microbiota and DTC remains unexplored.MethodsGenome-wide association study (GWAS) summary databases were utilized to select exposures and outcomes. The Mendelian randomization (MR) method was employed to investigate the causal relationship between the gut microbiota and DTC. A sensitivity analysis was performed to assess the reliability of the findings.ResultsFour bacterial traits were associated with the risk of DTC: Class Mollicutes [odds ratio (OR) = 10.953, 95% confidence interval (95% CI): 2.333–51.428, p = 0.002], Phylum Tenericutes (OR = 10.953, 95% CI: 2.333–51.428, p = 0.002), Genus Eggerthella (OR = 3.219, 95% CI: 1.033–10.024, p = 0.044), and Order Rhodospirillales (OR = 2.829, 95% CI: 1.096–7.299, p = 0.032). The large 95% CI range for the Class Mollicutes and the Phylum Tenericutes may be attributed to the small sample size. Additionally, four other bacterial traits were negatively associated with DTC: Genus Eubacterium fissicatena group (OR = 0.381, 95% CI: 0.148–0.979, p = 0.045), Genus Lachnospiraceae UCG008 (OR = 0.317, 95% CI: 0.125–0.801, p = 0.015), Genus Christensenellaceae R-7 group (OR = 0.134, 95% CI: 0.020–0.886, p = 0.037), and Genus Escherichia Shigella (OR = 0.170, 95% CI: 0.037–0.769, p = 0.021).ConclusionThese findings contribute to our understanding of the pathological mechanisms underlying DTC and provide novel insights for the clinical treatment of DTC.