摘要:Pericarpium Citri Reticulatae (PCR), the mature fruit peel of Citrus reticulata Blanco and its different cultivars, is an important citrus by‐product with beneficial health and nutritive properties. However, due to the lack of value‐added methods for its development and utilization, a large amount of PCR is discarded or wasted. To explore a possibly more effective method to utilize PCR, we compared the chemical and biological differences before (CK) and after (CP) microbial transformation of PCR by Aspergillus niger . UPLC‐ESI‐MS/MS, HPLC, and LC‐MS methods were used to compare the chemical profiles of CK and CP. The results demonstrated that microbial biotransformation by A. niger could transform flavonoid compounds by utilizing the carbohydrate and amino acid nutrients in PCR. This could also promote the accumulation of polyhydroxyflavones compounds in CP. The antioxidant assay demonstrated that CP had significantly greater free radical‐scavenging activity than CK. The higher antioxidant activity of CP may result from the high level of flavonoids with associated phenolic hydroxyl groups. Microbial biotransformation is an effective method for improving the antioxidant capacity of PCR and may be effective and useful in other natural product situations.