Drought is a global issue that has increasingly garnered worldwide attention. Glucosinolates (GSLs) are significant sulfur-containing compounds in cruciferous plants such as pakchoi (Brassica rapa L. ssp. chinensis), and their primary biological functions are exerted through their hydrolysis products. Allyl isothiocyanate (AITC), which is one of the degradation products of GSL, plays a crucial role in plants’ response to environmental stresses. To date, the drought-resistant mechanism of AITC has not been fully explored. This study investigated the effects of spraying different concentrations of AITC solutions (1 mM and 10 mM) on the growth parameters, stomatal characteristics, antioxidant indices, and glucosinolate metabolism of pakchoi under drought stress, compared to a control group treated with distilled water. The results shown that under drought stress, AITC spraying enhanced the plant's water retention capacity and restored their growth by promoting stomatal closure and improving photosynthetic capacity in pakchoi; mitigated oxidative stress damage and augmenting the plant's water absorption by increasing the activities of antioxidant enzymes and the concentrations of osmoregulatory substances in pakchoi; the application of AITC restored the glucosinolate metabolism in pakchoi, inhibiting the downregulation of genes associated with GSL synthesis and the upregulation of genes related to degradation that is induced by drought stress, thereby maintaining the balance between GSLs and ITCs.. In conclusion, AITC application alleviated the inhibition of pakchoi growth under drought stress by fostering stomatal closure, bolstering antioxidant defenses, and modulating glucosinolate metabolism.