The flat peach is a high economic value table fruit possessing excellent quality and a unique aroma. This article investigated the quality characteristics and aroma fingerprinting of flat peaches (Qingpan, QP; Ruipan 2, R2; Ruipan 4, R4; Wanpan, WP) from Xinjiang in terms of taste, antioxidant capacity, and volatile aroma compounds using high-performance liquid chromatography (HPLC) and HS-SPME-GC-MS. The results showed that the flat peaches had a good taste and high antioxidant capacity, mainly due to the high sugar–low acid property and high levels of phenolic compounds. This study found that sucrose (63.86~73.86%) was the main sugar, and malic acid (5.93~14.96%) and quinic acid (5.25~15.01%) were the main organic acids. Furthermore, chlorogenic acid (main phenolic compound), epicatechin, rutin, catechin, proanthocyanidin B1, and neochlorogenic acid were positively related to the antioxidant activity of flat peaches. All flat peaches had similar aroma characteristics and were rich in aromatic content. Aldehydes (especially benzaldehyde and 2-hexenal) and esters were the main volatile compounds. The aroma fingerprinting of flat peaches consisted of hexanal, 2-hexenal, nonanal, decanal, benzaldehyde, 2,4-decadienal, dihydro-β-ionone, 6-pentylpyran-2-one, 2-hexenyl acetate, ethyl caprylate, γ-decalactone, and theaspirane, with a “peach-like”, “fruit”, and “coconut-like” aroma. Among them, 2,4-decadienal, 2-hexenyl acetate, and theaspirane were the characteristic aroma compounds of flat peaches. The results provide a theoretical basis for the industrial application of the special aroma of flat peaches.