Metabolomics is a commonly used method to study the responses of organisms to environmental changes. However, the relationships between metabolites and biological endpoints still need further discussion. In this study, we exposed wheat seeds to sulfamethoxazole (0, 1, 10, 100 mg/L) for 5 days. The results show that sulfamethoxazole (SMX) had an inhibitory effect on wheat growth. It reduced shoot length, root length, shoot fresh weight, root fresh weight, chlorophyll content, and carotenoid content. At the same time, it increased the concentration of reactive oxygen species, the activity of superoxide dismutase, the activity of peroxidase, and the activity of catalase in the root. An orthogonal partial least squares analysis and correlation analysis were performed. SMX transformed five key metabolic pathways. Notably, certain metabolic alterations exhibited negative correlations with reactive oxygen species (ROS) accumulation and antioxidant enzyme activities (including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)), while showing positive associations with root growth parameters (fresh weight and length). Conversely, other metabolic changes appeared to promote ROS generation and enhance antioxidant enzyme activities, consequently inhibiting root growth. These findings offer novel perspectives on the metabolic regulation of wheat’s stress response to SMX exposure.