Selenium (Se) is a vital trace element for human health, and its uneven distribution in soil triggers Se deficiencies in some regions. Se biofortification has been demonstrated to mitigate this issue by producing Se-enriched crops. Chives (Allium schoenoprasum cv. 'sijixiaoxiangcong'), a simple-to-cultivate and fast-growing vegetable, offers a promising Se-accumulation ability. However, the physiological and molecular mechanisms underlying Se responses in chives remain unclear. This study applied sodium selenite at various doses to chives via root irrigation, and integrated strategies including multi-omics were employed to unfold the response mechanism. (1) Physiological data reveal that sodium selenite irrigation adversely affects the height, shoot weight, chlorophyll, and soluble sugar content of chives' aerial parts. However, chives exhibit a remarkable ability to accumulate selenium, reaching up to 40.21 mg kg