Blueberry fruit quality is characterized by multi-dimensional traits such as color, sugar-acid flavor, and volatile aroma. However, variations in progeny metabolites during seedling selection need further study. This research used the blueberry variety ‘Baldwin’ (BW) and its seedling offspring (BWSO) to compare fruit appearance, as well as sugar and acid components, anthocyanin monomers, and volatile metabolites. High-performance liquid chromatography was used to analyze anthocyanins, sugars, and acids, and gas chromatography–mass spectrometry was used to analyze volatile compounds. The results showed that, compared with BW, BWSO had a blacker skin and a lower L* value. Its total anthocyanin content increased by 35.90%, with delphinidin increasing the most (52.70%); component ratios were reconstructed. The main organic acids in BWSO decreased; titratable acid dropped by 29.82%, and the total soluble solids–acid ratio rose by 37.49%, indicating a good low-acid, high-sugar flavor. Forty-three differential volatile metabolites were found, and BWSO differed from BW in its green, fruity, and floral flavors. Notably, BWSO’s vitamin C (Vc) content decreased by 70.45% compared to BW, and Vc was negatively correlated with anthocyanin components. In conclusion, BWSO exhibits a black phenotype due to elevated total anthocyanins and restructured component ratios. Its low-acid trait yields better taste, but the antagonism between anthocyanin and Vc means balanced nutritional quality selection is crucial in dark-blueberry breeding. These findings offer new insights into the mechanism of color variation and provide a reference for balanced quality trait selection in seedling selection.