Mitochondria serve as the primary energy suppliers in cells, while also functioning as centers of immune regulation. The active compounds in gardenia may protect mitochondria, thereby exhibiting anti-inflammatory properties. This study measured the pro-mitophagy activities of nine representative components in gardenia, including geniposide and genipin, using flow cytometry. The effects of the key ingredient, genipin, on changes in mitochondrial membrane potential, mitochondrial mass, mitochondrial superoxide, and anti-inflammatory activity were then evaluated. The results indicated that treatment with 10 μmol•L−1 genipin activated mitophagy in 78.91% and 18.96% of 293T and HeLa cells, respectively. Additionally, genipin dose-dependently activated mitophagy in both cell types and exerted a significantly stronger effect than the positive control at 40 μmol•L−1, resulting in the activation of mitophagy in more than 80% of cells. This study also found that incubation with genipin significantly increased the mitochondrial membrane potential by 1.11~1.15 times that of the control. Furthermore, genipin was observed to dose-dependently increase mitochondrial reactive oxygen species, possibly linked to its promotion of energy metabolism. The anti-inflammatory capacity of genipin was evaluated in THP1-ASC-GFP cells, and the results demonstrated that the number of ASC inflammatory vesicles was significantly reduced in a concentration-dependent manner by genipin. In conclusion, the study findings suggest that genipin may exert its anti-inflammatory effects by modulating mitochondrial function, thus offering a new perspective for a deeper understanding of its mechanism of action.