This study aimed to explore the anti-inflammatory and gut microbiota modulation potentials of flavonoid-rich fraction (PFF) extracted from fruits. The results showed that PFF markedly reduced the production of nitric oxide (NO), tumor necrosis factor α (TNF-α), and interleukin 6 (IL-6) in LPS-stimulated RAW 264.7 cells. Meanwhile, PFF treatment also effectively decreased the phosphorylation levels of MAPK, PI3K/Akt, and NF-κB signaling-pathway-related proteins (ERK, JNK, p38, Akt, and p65). Moreover, PFF had an impact on microbial composition and metabolites in a four-stage dynamic simulator of human gut microbiota (BFBL gut model). Specifically, PFF exhibited the growth-promoting ability of several beneficial bacteria, including , , , and , and short-chain fatty acid (SCFA) generation ability in gut microbiota. In addition, spectroscopic data revealed that PFF mainly contained five flavonoid compounds, which may be bioactive compounds with anti-inflammatory and gut microbiota modulation potentials. Therefore, PFF could be utilized as a natural anti-inflammatory agent or supplement to health products.