Abstract: This study investigated inter-individual variation in seed quality among 35 Ginkgo biloba L. trees to identify superior genotypes for nut production and value-added utilization. Twenty seed traits were quantified and analyzed for variability, trait correlation, and comprehensive quality evaluation through principal component and cluster analyses. Results revealed substantial variation among individuals, with intrinsic quality variability greater than external morphological characteristics. Using a probability grading approach, three individuals with exceptionally high flavonoid content, three with extremely high terpene lactone content, and one with extremely low ginkgolicacid content were identified as potential parental materials for breeding specialized germplasm and hybrid lines for medicinal and edible use. Fifty-four pairs of indicators exhibited highly significant correlations between morphological and biochemical quality traits, while four pairs showed significant correlations. Eleven major indicators (including eight phenotypic traits, three weight-related traits, and ginkgolic acid concentration) were identified as key determinants of seed quality. Ten individuals were distinguished by large fruit size and low ginkgolic acid content, indicating strong potential for targeted breeding, genetic improvement, and industrial application of nut-bearing Ginkgo biloba.