In this work, the phytochemical characterization, biological activity, and cytotoxic mechanism of aerial and rhizome methanol extracts (SME and RME) of Epimedium pubigerum were investigated to demonstrate its potential usage in the treatment of lung cancer. LC‐HRMS analysis, total phenolic/flavonoid content assay, DPPH radical scavenging assay, DNA interaction, cytotoxicity, and western blotting were investigated using different methods. Fumaric acid was found to be the most abundant compound in both extracts. SME and RME were cytotoxic on A549 cells concentration‐dependently. Also, in vitro scratch assay showed that SME and RME led to a significant anti‐migratory effect at 1 mg/mL. Cytochrome c, p53, and caspase 3 expression significantly increased in the presence of RME compared to the control. All of these results claimed that RME might be suggested as a theoretically more effective phytotherapeutic agent for lung cancer compared to the effect seen with the SME.