The widespread use of S-metolachlor (ME) in agriculture to suppress weeds and boost crop yields, particularly in cultivating Vigna angularis, is well established. However, the application of organosilicon adjuvants with herbicides has potential threats to non-target crops. This study investigates the toxicity symptoms and mechanisms when V. angularis is exposed to ME in conjunction with a common organosilicon adjuvant. Results indicate that ME inhibits the growth of V. angularis seedlings, and adding adjuvants could aggravate the negative effects of ME. According to the growth index of seedlings, the adjuvant increased the toxicity of ME by 84–96 %. Additionally, the chlorophyll content, root permeability, and antioxidant indicators in the seedlings were also adversely affected. Integrated metabolomics and transcriptomics analyses reveal that differentially abundant metabolites (DAMs) and differentially expressed genes (DEGs) are mainly enriched in four ways: "lysine degradation," "ABC transporters," "phenylalanine metabolism," and "monoterpenoid biosynthesis." The metabolic pathways and gene regulatory network involving 11 DAMs and 22 DEGs are associated with the physiological processes affected by ME and the adjuvant. This study provides guidance for the application of herbicides and their adjuvants in agricultural production to minimize adverse effects on non-target crops.