Chlorogenic acid, an important active component of coffee with anti-tumor activities, has been found for a hundred years. However, the lack of understanding about its target proteins greatly limits the exploration of its anti-tumor molecular mechanisms and clinical applications. Here, in vitro and animal experiments showed that chlorogenic acid had a significant inhibitory effect on the proliferation of A549 cells. The ability of chlorogenic acid to naturally emit fluorescence was exploited to screen its target proteins while avoiding false positives brought about by chemical modifications when using fluorescent tags. Consequently, we identified and verified annexin A2 as a covalent binding target of chlorogenic acid in A549 cells. We also discovered that chlorogenic acid inhibits the binding of annexin A2 to p50 subunit thereby inhibiting the expression of downstream anti-apoptotic genes cIAP1 and cIAP2 of the NF-κB signaling pathway in A549 cells in vitro and in vivo. Moreover, we found that chlorogenic acid hindered the binding of annexin A2 to actin possibly causing inhibition of tumor cell cycle and migration. Thus, this work demonstrates that chlorogenic acid binds annexin A2, causing a decrease in the expression of NF-κB downstream anti-apoptotic genes, and inhibiting the proliferation of A549 cells in vivo and in vitro.