Metamitron (MTM) is a typical and widely used triazine herbicide in agricultural production. Its moderate toxicity and high residue in the environment have deleterious impacts on human health. The establishment of a rapid and efficient MTM detection method is of great significance. In this study, a magnetic-bead SELEX (systematic evolution of ligands by exponential enrichment) system was developed to select the MTM aptamers with high affinity and specificity. Through 10 rounds of screening, six candidate aptamers with the highest abundance were obtained by high-throughput sequencing. The homology, secondary structure, and affinity analyses were performed. The aptamer named MTM-6 was selected as the optimal aptamer with the dissociation constant (Kd) value of 16 nM. Then, a colorimetric detection method for MTM based on aptamer MTM-6 and the aggregation of gold nanoparticles (AuNPs) induced by NaCl was established with a linear range from 20 to 1000 nM (R = 0.9966) and a limit of detection (LOD) of 4.58 nM. The average recovery rate of MTM in the application of actual aqueous samples ranged from 95.40 to 107.83% with a relative standard deviation (RSD) from 1.11 to 3.48%. With considerable sensitivity and specificity, this colorimetric aptasensor is convenient and efficient, and shows bright application potential in MTM detection in aqueous samples.