To investigate the quality variations of prune vinegar during fermentation, multivariate statistical analysis (MSA) was used in conjunction with high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS). The results showed that the pH decreased slightly, there was a rapid decline in sugar content, and a gradual increase in total acid content, which achieved stabilization at 3.68 g/100 mL. The content of organic acid increased, while the total phenol content decreased. The total flavonoid content did not change significantly. Furthermore, the antioxidant capacity initially decreased and then increased. Prune vinegar contains important phenolics such as rutin, resveratrol, salicylic acid, trans-ferulic acid, and (+)-catechin. In addition, the flavor of prune fruit vinegar underwent changes during the fermentation process. During the fermentation of fruit vinegar, large quantities of 2,3-butanediol, glacial acetic acid, nonanoic acid, ethyl acetate, ethyl heptanoate, ethyl caproate, and linalool were produced. These compounds give prune vinegar its distinctive fruity and floral aroma. This study provided a comprehensive framework for the efficient processing of prunes and a strategy for enhancing the quality characteristics of prune vinegar or other fermented products.