The higher acidity in fruits compared with grapes was one of the main obstacles to producing high-quality fruit wines. In the present research, the effect of the split batch fermentation pattern on the metabolites of greengage wines was investigated. This fermentation pattern included whole fruit immersion in the sucrose and coculturing Saccharomyces bayanus Y4 with Torulaspora delbrueckii Y7. These results showed that the contents of total acidity and dominant organic acids were significantly reduced among the batches. Aliphatic compounds were decreased with the batches, while aromatic compounds that contributed to flavor improvement were increased oppositely. The acetate esters, ketones, and terpenes contents were significantly increased in the first batch of coculture. In addition, acidic stress largely affected the kinetics characteristics of greengage wine on a pilot scale. Interestingly, the increment of total acidity was closely associated with the rate of total sugar consumption, which was affected by microbial activities. The acidity content was significantly declined and distinct flavour profiles were formed in split batch and coculture fermentation of greengage wines. It provides a new avenue to enhance the flavor and quality of fruit wines.