Abstract: This research investigated the alterations in functional properties and flavor quality of blueberry-collagen peptide beverage under different fermentation times (0~48 h). The fermented beverage was produced through yeast fermentation using blueberry and cod skin collagen peptides. Subsequent analyses involved determining the nutrient composition (polyphenols, flavonoids, anthocyanins), digestive enzyme inhibitory activity (α-amylase and lipase), and free radical scavenging rate of the beverages. Meanwhile, gas chromatography-ion mobility spectrometry (GC-IMS), electronic tongue, electronic nose, and sensory evaluation were employed to assess the flavor modifications of the beverages throughout the fermentation process. The results revealed that the beverage attained peak levels of polyphenols (1.40 mg∙mL⁻¹) and flavonoids (1.22 mg∙mL⁻¹), with an anthocyanins retention of 0.043 mg∙mL⁻¹ after fermentation for 36 h. The free radical scavenging rate exceeded 80%, while the α-amylase and lipase inhibition rates were 55.17% and 43.69%, respectively. The GC-IMS analysis showed notable increases in esters such as methyl propionate, isoamyl acetate, and ethyl caproate, as well as alcohols like isoamyl alcohol, isobutanol, and n-propanol, whereas sulfide-containing compounds such as allyl isothiocyanate and diethyl trisulfide exhibited decreased levels. These results demonstrated that the blueberry-collagen peptide beverage, after 36 h of fermentation, significantly enhanced active component content, antioxidant capacity, and digestive enzyme inhibitory activity. The production of fruity esters/alcohols and the degradation of sulfur-containing off-flavor substances were promoted. By optimizing fermentation time to regulate the directional accumulation of yeast metabolites, this research achieved synergistic optimization of functional properties and flavor quality, presenting a novel approach for enhancing the value of blueberry resources and advancing the development of collagen-based beverages.