In the study, gas chromatography-ion mobility spectrometry (GC-IMS) coupled with electronic nose and sensory evaluation was used to analyze the change of volatile compounds in blue honeysuckle-blueberry juice mixture during fermentation, and key aroma compounds were identified by the combined use of orthogonal partial least squares discriminant analysis (OPLS-DA) and odor activity values (OAV). Meanwhile, the changes in nutritional quality were analyzed by measuring physicochemical properties, active compounds and antioxidant capacity. The results showed that the flavor of blue honeysuckle-blueberry juice mixture was significantly enhanced after fermentation for 24 hours, and the fruity aroma, fermented aroma and aftertaste were enriched. A total of 58 volatile compounds were identified by GC-IMS, including esters, aldehydes, alcohols, ketones and furans. After fermentation, the contents of various flavor compounds such as esters (e.g., methyl propionate and ethyl butyrate) and alcohols (e.g., isoamyl alcohol and n-hexanol) significantly increased, synergistically contributing to a blend of fruity, floral and fermented aromas. Additionally, fermentation led to a reduction in the contents of aldehydes and sulfides, thereby weakening the grassy and pungent odors and consequently resulting in a more harmonious flavor profile. The OPLS-DA and OAV analyses identified butyl acrylate, ethyl hexanoate, isoamyl acetate, ethyl butyrate, ethyl valerate, 2-formylpyrrole, 3-hepten-2-one, and isopentyl alcohol as differential characteristics flavor compounds after fermentation. The juice turned from black-purple to brighter red-purple, while the contents of active compounds such as polyphenols, ascorbic acid, and antioxidant levels were maintained at a high level. The juice maintained good quality, and the flavor was significantly enhanced after yeast fermentation for 24 hours. This study confirms that co-fermentation of two fruits can break through the limitation of a single raw material, providing a theoretical basis for the development of functional fermented fruit juice with good nutrition and flavor and being of practical significance for innovation in deep-processing technology and high-value utilization of resources.