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In this study, we aimed to investigate the molecular mechanisms underlying the differences between white or purple Platycodon grandiflorus, through integrated metabolomic and transcriptomic analyses. The results reveal that we identified 3 differential metabolites. A specific delphinidin-based anthocyanin with the molecular formula C₆₃H₇₃O₃₇ accumulates significantly higher in purple flowers, which is markedly increased by 1504.16-fold compared with white flowers. In contrast, white flowers predominantly accumulate a flavone-type compound (C₂₇H₁₇NO₄) and obetyolin (C₂₀H₂₈O₈ ), and the contents of these two compounds are decreased by 2.04-fold and 1.70-fold, respectively. The contents of compounds C₆₃H₇₃O₃₇ and C₂₇H₁₇NO₄ show extremely significant variation (P < 0.01), while lobetyolin C₂₀H₂₈O₈ exhibited significant differences (P < 0.05). A total of 1970 DEGs were identified between white or purple Platycodon grandiflorus. Comparative transcriptomic analysis reveals differential expression of genes and transcriptional regulators involved in flower color formation between white and purple Platycodon grandiflorus flowers. The DEGs showing differential expression between white and purple flowers include PgCYP75A6, PgF3GT1, PgAN3, PgCYP98A2, PgBGLU18 and PgCYP73A12. The expression pattern of the transcription factors PgMYB4, PgbHLH2, PgWRKY44, PgARPC1A, and PgHARBI1 also showed differences that aligned with the flower color. In summary, the study provided a theoretical foundation for the genetic improvement and breeding of Platycodon grandiflorus varieties. In summary, this study the in-depth exploration of key genes regulating floral color and lays a solid foundation for the subsequent breeding of Platycodon grandiflorus varieties.