【Objective】This study compared the nutritional quality between Allium cepa L.var.agrogatum Don.and Allium cepa L.to improve the further study of Allium cepa L.var.agrogatum Don..【Method】Pink-peel and yellow-peel Allium cepaL.var.and brown-peel and yellow-peel skin Allium cepa L.agrogatum Don.were chosen in this study,and their nutritional compositions and flavor compounds of outer-bulb and inner-bulb were measured and analyzed.【Result】The mass fraction of day matter and the contents of soluble sugar,soluble protein,free amino acids,pyruvate,and flavonoids in Allium cepaL.var.agrogatum Don.were 9.37%-19.20%,89.34-132.99 mg/g,1.54-2.46 mg/g,1.56-2.85μg/g,62.31-123.67μmol/mL,and 2 193.4-2 648.2 mg/kg,respectively.Inner layer had higher contents of basic nutritional components and pyruvate but lower flavonoids than outer layer.The nutrients of brownpeel Allium cepaL.var.agrogatum Don.were higher than yellow-peel skin Allium cepaL.var.agrogatum Don.except soluble sugar and pyruvate.【Conclusion】The basic nutritional compositions and special flavormaterials of Allium cepa L.were significantly lower than those of Allium cepa L.var.agrogatum Don..Nutrient compositions contents were different between different peel color onions,and their contents in inner layer were higher than those of outer layer except flavonoids.