To further explore the mechanism of âthe longer storage time, the better bioactivityâ of aged Guang Chenpi, the dry pericarp of Citrus reticulata âChachiâ (CRC), a series of activity assessments were performed on spleen deficiency mice. The constituents in CRC with different storage years were analyzed by LCâQâOrbitrap/MS. A total of 53 compounds were identified, and CRC stored for more than 5âyears showed higher flavonoid content, especially that of polymethoxyflavones. Antiâspleen deficiency bioactivity analysis among various CRC with different storage years showed aged CRC (stored for more than 3âyears) could significantly alleviate fatigue and depression behaviors much better, increase Dâxylose and gastrin secretion, and upregulate the expression of the linking protein occludin in the colon walls. Results from 16S rDNA sequencing showed that aged CRC could downregulate the abundance of Enterococcus, Gemmata, Citrobacter, Escherichia_Shigella, and Klebsiella, which were significantly overrepresented in the model group. Bacteroides, Muribaculum, Alloprevotella, Paraprevotella, Alistipes, Eisenbergiella, and Colidextribacter were downregulated in the model group but enriched in the CRC groups. At last, the spectrumâeffect relationship analysis indicated that flavonoids such as citrusin III, homoeriodictyol, hesperidin, nobiletin, and isosinensetin in aged CRC showed the highest correlation with better activity in ameliorating spleen deficiency by regulating gut microbiota. Flavonoids contribute most to discriminating aged CRC and could disclose the basis of âthe longer storage time, the better bioactivityâ of aged Guang Chenpi.