Different varieties of apples exhibit diverse characteristics in flavor and other edible qualities, which directly affect consumer expectation and purchase intention. In this study, the mechanism of apple flavor quality formation was investigated by six cultivars from Weihai, China. Results indicated that the flavor quality, including sweet, sour taste and fruity, floral notes, was most influenced by apple varieties. A high level of key volatile compounds in Venus Golden apple (VG) could promote the development of unique fruity and sweet aromas, such as amyl acetate, hexanal, 2-methylbutyl acetate, hexyl acetate, etc. Meanwhile, the genetic background significantly influenced the quality traits of apples by the metabolic profile and pathway. The enrichment of amino acid and carbohydrate metabolic pathways is crucial for biosynthesis of flavor compounds. This study uncovers the molecular basis of excellent edible qualities in apples and provides guidance for the selection, breeding, and marketing of superior apple varieties.