Previous epidemiological and experimental studies have yielded conflicting results regarding the influence of human micronutrient levels on the risk of colorectal polyps (CP). In our study, we conducted a two-sample Mendelian randomization (MR) investigation to probe the link between 13 human micronutrients (calcium, selenium, magnesium, phosphorus, folate, vitamins B-6, B-12, C, D, beta-carotene, iron, zinc, and copper) and the genetic susceptibility to CP. Summary statistics for CP (n=463,010) were obtained from pan-European genome-wide association studies, and instrumental variables for 13 micronutrients were screened from published genome-wide association studies (GWAS). After selecting suitable instrumental variables, we performed a two-sample MR study, deploying sensitivity analyses to judge heterogeneity and pleiotropy, using inverse variance weighted methods as our primary estimation tool. Our study identified that a genetic predisposition to elevated toenail and circulating selenium or serum β-carotene concentrations lowers the risk of CP occurrence. However, no statistically significant association was observed between the other 11 micronutrients and the risk of CP. The study findings provide evidence that the micronutrient selenium and β-carotene may confer protective effects against the development of CP.