<p>This research offers an in-depth analysis of the influence of ploidy levels on the morphological characteristics and fundamental quality traits of haskap (<i>Lonicera caerulea</i> L. subsp. <i>edulis</i> (Turcz. ex Herder) Hultén) fruits, contributing critical scientific insights for their cultivation, breeding, and market application. By examining fruits from different ploidy levels collected from Hokkaido University’s Experiment Farm during 2022–2023, this study highlights the significant variability in fruit weight, volume, peel thickness, seed weight, and sugar content among diploid, tetraploid, pentaploid, aneuploid, and hexaploid fruits. Notably, tetraploid fruits exhibited superior morphological traits, while aneuploid fruits stood out for their sugar content. Statistical analyses, encompassing multiple comparisons, correlation analysis, and principal component analysis, revealed significant correlations between traits related to fruit size and market value, in addition to the relationship between ploidy levels and structural features like peel thickness. These findings emphasize the importance of considering ploidy in haskap breeding and cultivation to enhance yield and fruit quality according to market demands. Additionally, this study suggests that ploidy manipulation may influence fruit structural traits such as peel thickness, which are potentially related to the plant’s physical defense, opening new avenues for future research on the effects of ploidy variation on bioactive components and the health benefits of haskap fruits. The study provides valuable guidance for haskap cultivation and breeding. It extends its implications to other crops, suggesting that precise control of ploidy variations can significantly impact crop yield, quality, and adaptability to environmental and market changes.</p>