Dinuclear Ni(II) macrocyclic complex A ([Ni2L1OAc]ClO4⋅CH3OH⋅H2O) and dinuclear Ni(II) acyclic complex B ([Ni2L2](ClO4)2) were synthesized by condensation between H2L (3,3′‐(ethane‐1,2‐diylbis(benzylazanediyl))bis(methylene)bis(2‐hydroxy‐5‐methyl‐benzaldehyde)) and different molar equivalent 1,3‐propanediamine in the presence of Ni(II) ions. The structures of complexes were characterized by IR spectroscopy, elemental analysis, electrospray mass spectra and X‐ray single crystal diffraction. In complex A, the Ni(II)‐Ni(II) distance was 2.9413(7) Å, bridged by two phenolic oxygens and an acetate anion, while in complex B, it was 3.0540(1) Å, only bridged by two phenolic oxygens. The calf thymus DNA (CT‐DNA) binding ability was studied through spectroscopic and electrochemical methods, the corresponding binding constant for complexes A and B were 6.45×104 M−1 and 8.65×104 M−1, respectively. The MS revealed that B can transform to A by adding more H2L, and A cannot transform to B in the presence of excess 1,3‐propanediamine.