Abstract: In this study, four representative varieties of watercored apples (Fuburuisi, Meima Fuji, Yanfu No. 3, and Yanfu No. 8) from the Zhaotong production area of Yunnan were selected as research subjects. The differences in watercore and nutritional quality among the four apple varieties were explored through measurements of watercore index, color, flavor, and nutritional components. The results indicated that the watercore degree was highest in Fuburuisi and lowest in Meima Fuji. In terms of appearance, Yanfu No. 3 was observed to have the darkest peel color, while Fuburuisi exhibited the darkest flesh color. Yanfu No. 8 was found to have the lightest peel color, while Meima Fuji was found to have the lightest flesh color. Regarding taste, Meima Fuji was characterized by the highest soluble solid-to-acid ratio. In terms of aroma, Yanfu No. 3 and Yanfu No. 8 were shown to have highly similar aromatic profiles, whereas Fuburuisi contained the most diverse and abundant volatile compounds. Concerning nutritional components, higher phenolic and total flavonoid contents were detected in Fuburuisi and Yanfu No. 3 compared to Meima Fuji and Yanfu No. 8, and the highest vitamin C content was recorded in Yanfu No. 3. Through correlation analysis, it was determined that watercore was highly correlated with flesh color, a higher degree of watercore was associated with darker and more reddish-yellow flesh, although no correlation was found with peel color. The watercore index was found to be strongly associated with apple flavor, exhibiting positive correlations with total soluble solids (TSS), titratable acidity (TA), malic acid, and sorbitol content, but negative correlations with pH, soluble solid-to-acid ratio, starch, and quinic acid content. In terms of volatile compounds, the watercore index was positively correlated with aldehydes and terpenes but negatively correlated with esters. Regarding nutritional components, watercore was positively correlated with flavonoid and phenolic content. Comprehensive analysis suggested that watercore not only contributes to darker flesh coloration but also influences taste and aroma. Moreover, apples with higher watercore exhibited greater nutritional value.