To address flavor loss in Xinjiang flat peach processed products caused by thermal processing, this study investigated the effects of different sterilization methods on flavor compounds in yellow flat peach juice and explored characteristic flavor reconstruction technology based on flavor fingerprinting. Using yellow flat peaches as raw material, pasteurization (PS), high-temperature short-time pasteurization (HTST), and ultrasonic sterilization (US) treatments were applied. Physicochemical indicators and flavor compounds were measured via HPLC, HS-SPME-GC-MS, and molecular sensory techniques. Results indicate: Thermal sterilization reduced soluble solids (1.73% in PS group, 3.59% in HTST group) and significantly increased quinic acid among organic acids (10.57% in PS group, 4.68% in HTST group, 3.83% in US group), while malic acid decreased by 6.79% in the HTST group. Total amino acids increased by 2.52 and 1.03 g/kg in PS and HTST groups, respectively, while decreasing by 0.89 g/kg in the US group. Umami amino acids constituted the highest proportion (78.63%-81.32%). Total volatile compounds decreased significantly. Alcohols increased by 1.38% and 0.71% in the PS and US groups, respectively, while aldehydes decreased by over 9%. Key aroma compounds like n-hexanol and hexanal diminished, while off-flavor compounds such as 1-octen-3-one and β-damascenone accumulated. After replenishing key aroma compounds based on characteristic aroma fingerprint spectra, the typical aroma of flat peach juice was restored, while cooking odors and off-flavors were significantly reduced. This study provides a theoretical basis for enhancing the flavor of flat peach processing products, demonstrating that ultrasonic sterilization is more effective than thermal sterilization in preserving natural flavor.