Storey onion (Allium cepa L. var. proliferum Regel) is a variety of onion commonly grown in northern China that has not been researched in detail. This study aimed to identify the chemical compositions of storey onion aqueous extracts by UPLC-ESI-MS/MS, as well as characterize the antioxidant, antibacterial and cytotoxic activities, compared with welsh onion and onion. A total of 42 compounds were identified, among which the contents of organosulfur compounds (962.20 ± 34.55 μg/g), polyphenols (100.40 ± 12.55 μg/g) and organic acids (54.04 ± 2.69 μg/g) in storey onion were higher than those in welsh onion and onion. Additionally, the contents of cycloalliin (551.74 ±8.12 μg/g), ajoene (159.31 ±5.30 μg/g) and (E)-1-propene-1-sulfenic acid (72.12 ±2.98 μg/g) in storey onion were the highest. Storey onion had pronounced DPPH• (IC₅₀=1.24 ±0.52 mg/mL) and OH• scavenging activities (IC₅₀=14.45 ±1.29 mg/mL) as well as ferric ion reducing power (absorbance from 0.32-2.21). Onion had the highest ABTS•⁺ scavenging activity (IC₅₀=1.64 ±0.64 mg/mL), while welsh onion had the lowest antioxidant activity. Storey onion had the strongest inhibitory effect on all the tested strains (MIC 31.3-125 mg/mL), and cell viability assays against human liver (HepG2) cancer cell lines also illustrated that aqueous extracts from storey onion significantly inhibited cell proliferation (when incubated for 24 h, IC₅₀=33.21 ±1.12 mg/mL) and induced cell apoptosis. Welsh onion and onion also had weaker antibacterial and anticancer activites, with those of onion being the weakest. The results showed that storey onion with excellent biological activity may benefit to human health and can be developed into functional foods.