A series of polyoxometalate-based cyclophanes (polyoxometalatocyclophanes) were synthesized via covalent linkage of Lindqvist-type hexamolybdate clusters with bis-arylimido ligands bearing flexible alkyl chains. Single-crystal X-ray diffraction and circular dichroism spectroscopy confirm that compound 3, ((n-C₄H₉)N)₂[Mo₆O₁₇N(o-phenyl-O(CH₂)₅O-phenyl-o)N], undergoes spontaneous chiral resolution upon crystallization. Biological evaluation against the leukemia K562 cell line shows that, among the tested compounds, including aromatic amine ligands, hexamolybdate salts, and related polyoxometalatocyclophanes, compound 3 exhibits the highest inhibitory activity. At higher concentrations, its activity surpasses that of the positive control, 5-fluorouracil (5-FU). Molecular docking and molecular dynamics simulations indicate that the [Mo₆O₁₇N(o-phenyl-O(CH₂)₅O-phenyl-o)N]²⁻ anion adopts a compact conformation and can effectively bind to the anti-apoptotic protein Bcl-2, with a predicted binding affinity of −27.39 kcal/mol.