In this study, changes in volatile compounds co-fermented by different Pichia kluyveri with Saccharomyces cerevisiae were analyzed using GC-IMS and compared with S. cerevisiae fermentation, to investigate the production of aroma in mulberry wine during the fermentation process. A total of 61 compounds were accurately identified, including 21 esters, 10 alcohols, 8 aldehydes, 6 ketones, and 19 other volatiles. Compared with the single strain fermentation (S. cerevisiae), the content of 2-methylpropyl acetate, allyl Isothiocyanate, ethyl crotonate, isobutyl propanoate, and butyl 2-methylbutanoate, co-fermentation groups (S. cerevisiae with different P. kluyveri) showed a significant decrease. Alcohols, aldehydes, ketones, and organic acid were lower in both the F(S-P1) and F(S-P2) groups than in the F(S) group throughout fermentation. The 2-methylpentanoic acid only was contained in the F(S) group. The co-fermentation with different P. kluyveri could also be well distinguished. The content of Benzaldehyde and 4-methylphenol in the F(S-P1) group was significantly lower than that in the F(S-P2) group. The PCA results revealed effective differentiation of mulberry wine fermented by different fermentation strains from GC-IMS. The result showed that P. kluyveri could establish a new flavor system for mulberry wine, which plays a crucial role in enhancing the flavor of fruit wine.