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A series of dioxidomolybdenum (VI) complexes, [MoO2(ESB)H2O]·DMF (1), [MoO2(ESB)MeOH] (2), and [MoO2(ESB)H2O]·EtOH (3), containing 3‐ethoxysalicylaldehyde benzoylhydrazone have been synthesized and analysed using various spectral and analytical techniques such as elemental analyses, IR spectra, UV–Vis absorption spectra, X‐ray crystallography, and Hirshfeld surface analysis. Based on the elemental and spectral analysis, six‐coordinate geometry was assigned for these complexes wherein the hydrazone ligand binds to the metal centre in its dianionic enolate form through ONO donor set. Distorted octahedral geometry of complexes 1 and 2 was evidenced from their crystal structures, which is typical for many cis‐dioxido complexes of MoVI. The proligand and the new complexes were examined for their DNA binding, DNA cleavage, and cytotoxic properties. The DNA binding efficiency of the compounds in terms of their binding constants (Kb) of the metal complexes was observed to be 1.3727 × 105 M−1, 3.0194 × 104 M−1, and 1.13206 × 104 M−1 for [MoO2(ESB)H2O]·DMF (1), [MoO2(ESB)MeOH] (2), and [MoO2(ESB)H2O]·EtOH (3), respectively, indicating that these complexes strongly bind to DNA. To determine the binding interactions of the complexes with DNA and protein (BSA), molecular docking studies were carried out. Gel electrophoresis study reveals the fact that the complexes cleaved supercoiled pUC‐18 DNA to nicked form (Form II) in the presence and absence of H2O2. The complexes showed significantly high cytotoxicity against MCF‐7 (breast cancer cells). [ABSTRACT FROM AUTHOR]