•We simulated the reaction between telomerase and helenalin using QM/MM method.•The CYS445 residue was reversibly alkylated by helenalin.•A hydrogen bond was formed between the LYS416 residue and helenalin in the reaction.•The LYS416 residue is vital to the recognition between telomerase and DNA.•Thus, helenalin inhibits telomerase by interfering with the recognition of DNA.Enhanced telomerase activity is a hallmark in the majority of cancer cells. Thus, understanding the interactions between telomerase and its inhibitors is fundamentally important for the development of novel anticancer drugs without severe side effects. In this study, the covalent binding of helenalin to CYS445 of telomerase (PDB ID: 3DU6) was simulated using combined quantum chemical and molecular mechanical (QM/MM) methods. The results showed that the reaction was a reversible Michael-type addition and a hydrogen bond was formed between helenalin and the side chain of LYS416 of telomerase during the reaction procedure. The LYS416 residue is vital to telomere DNA recognition by interacting with DNA base through hydrogen bonds. The alkylation of CYS445 of telomerase by helenalin may interfere with the telomere DNA recognition at the telomerase active site, thus resulting in inhibition of the enzyme activity.