Flavonoid biosynthesis is proposed to play a critical role in floral organ development in Paeonia species. However, its specific involvement in stamen petalization remains unclear. This study identified and characterized 13 gene families related to flavonoid biosynthesis across four Paeonia species. Comparative and phylogenetic analysis revealed that most flavonoid biosynthesis-related genes experience lineage-specific expansion in P. ludlowii. Genes belonging to the same family were commonly clustered on chromosomes and displayed highly conserved domain and motif compositions. The cis-element analysis identified Cis-acting elements associated with light, hormonal, and stress responses, implicating their regulatory roles in flavonoid biosynthesis. To further investigate the role of these genes in stamen petalization of P. lactiflora, expression profiling analyses were performed on ‘Fen Yu Nu’ (normal stamens) and ‘Lian Tai’ (petaloid stamens) cultivars using transcriptomic data released previously. Three quercetin-related genes revealed distinct stage-specific patterns in ‘Fen Yu Nu’ and ‘Lian Tai’. Notably, PlaF3’H03 exhibited significant upregulation during petaloid stamen development in ‘Lian Tai’, suggesting its role in stamen transformation. Molecular docking identified PlaF3’H07 as a key enzyme with strong substrate-binding affinity (ΔG = −4.7 kcal/mol), supporting its catalytic function in quercetin synthesis. The expression pattern of key flavonoid biosynthetic genes was also confirmed across three developmental stages of floral buds by real-time quantitative PCR. This study provides insights into the genetic basis underlying stamen petalization in P. lactiflora and offers potential targets for genetic improvement of floral traits in Paeonia and other ornamental plants.