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The dynamic changes of physicochemical properties, flavor and microbial communities in 1-, 3-, 5-, and 10-year aged Citri Reticulatae Pericarpium (CRP) was systematically analyzed, so as to reveal the quality formation mechanism of CRP. Results revealed that: (1) CRP color deepened progressively with time, total flavonoid content and antioxidant capacity of CRP significantly rose, total amino acids continuously decreased; (2)the main volatile compounds of CRP included alkenes, alcohols and esters, and it showed an initial accumulation followed by degradation trend, with 5-year aged CRP possessing the most complex flavor profile, where γ-terpinene, benzaldehyde, and nonanol served as key age-specific flavor compounds; (3) microbial diversity peaked in 5-year aged CRP, with Proteobacteria as the dominant bacterial phylum and Ascomycota as the dominant fungal phylum, while specific genera ( Vibrio , Xeromyces ) were significantly associated with aging stages; (4) correlation analysis demonstrated that fungi, particularly Aspergillus and Wallemia , showed stronger associations with physicochemical properties, antioxidant capacity, and flavor development, and were more strongly linked to complex acid, aldehyde, and ketone flavors, whereas bacteria were mainly associated with basic flavor formation. The traditionally recognized attribute of “older is better” for CRP, in terms of the investigated physicochemical, antioxidant, volatile, and microbiological indicators, appears to manifest through the dynamic integration of flavonoid accumulation, enhanced antioxidant capacity, optimized flavor compounds, and microbial community succession. The 5-year CRP represents a key transition phase for flavor complexity and microbial diversity (within the sampled aging intervals), while long-term aging promotes the enrichment of functional metabolites. This study elucidates the multidimensional evolutionary patterns of CRP aging, providing systematic data support and theoretical foundations for its quality assessment, age authentication, and mechanistic research. • The underlying mechanism of quality formation of Citri Reticulatae Pericarpium (CRP) during aging was explored. • The 5-year aged CRP showed the most complex flavor profile, with γ-terpinene, benzaldehyde and nonanol served as key flavor compounds. • The microbial diversity peaked in 5-year aged CRP, and the specific genera were significantly associated with aging stages. • Fungi dominated the regulation of physicochemical properties, antioxidant capacity, and flavor development of CRP.