The energy metabolism crisis is considered an important risk factor for severe influenza A virus (IAV) infection. During virus replication, the host cell’s “metabolic reprogramming” is beneficial for increasing the energy demand of the virus. SIRT1 plays a major role in altering metabolic reprogramming, and upregulation of SIRT1 expression can defend against viral infection. This study established a high-throughput drug screening method for human SIRT1 promoter. Nine natural medicines were selected from 134 traditional Chinese medicines. Among them, the activity ofGardenia jasminoidesEllis was relatively high. Further research has found that the plant extract and its active compound Genipin and its derivatives can significantly inhibit IAV replication, improve the survival rate of infected mice, and inhibit pneumonia. In addition, Genipin significantly increased the levels of energy metabolism core regulatory factors SIRT1, PPAR γ, PGC-1 α, and p-AMPK, inhibited IAV induced activation of MAPKs and NF-κB, and alleviated inflammatory response. The pharmacological antagonists of SIRT1 and PGC-1 α, as well as siRNA, significantly counteracted the effects of Genipin on IAV replication and inflammation. In summary, we found that Genipin and its derivatives could significantly inhibit IAV replication and inflammation, possibly by activating the AMPK-SIRT1-PGC-1α signaling pathway and altering metabolic reprogramming.