Onion（Allium cepa L.） is a very important vegetable crop widely cultivated throughout the world. In this study, we measured total anthocyanins and flavonols of onions of three colors. The fresh weight（FW） of total anthocyanins were（29.99±1.19）,（9.64±1.30） and（0.75±0.40） mg 100 g^–1 fruit in red, yellow and white onions, respectively. Likewise, the FW of total flavonoids were（111.10±5.98）,（36.64±3.59）, and 0 mg 100 g^–1 in red, yellow and white, respectively. Four types of anthocyanins（delphinidin 3,5-diglycosides, cyanidin 3,5-diglycosides, cyanidin 3-glycosides and cyanidin 3-（6′′-malonyl）-glucopyranoside） and two kinds of flavonoids（quercetin and quercetin 3-glycosides） were identified in two varieties（red and yellow bulb） of onions by HPLC/DAD-ESI/MS. The total polyphenol contents were also measured by means of Folin-Ciocalteu method. Moreover, all the concentrations of anthocyanins, flavonoids and polyphenols showed significantly positive correlations with antioxidant activities measured by DPPH˙, ABTS˙＋ and FRAP assays. This study provided information on anthocyanin and flavonoids compositions that will be useful for onion breeding.