Two new trinuclear hetero-metallic copper(II)–zinc(II) complexes [(CuL)2Zn(N3)2] (1A and 1B) have been synthesized using [CuL] as a so-called “metalloligand” (where H2L = N,N′-bis(salicylidene)-1,3-propanediamine) and structurally characterized. Complexes 1A and 1B have the same molecular formula but crystallize in different crystal systems (triclinic for 1A and monoclinic for 1B) with space group P for 1A and P21/c for 1B. 1A is an angular trinuclear species, in which two terminal four-coordinate square planar “metalloligand” [CuL] are coordinated to a central Zn(II) through double phenoxido bridges. The Zn(II) is in a six-coordinate distorted octahedral environment being bonded additionally to two mutually cis nitrogen atoms of terminal azide ions. In complex 1B, in addition to the double phenoxido bridge, the two terminal Cu(II) ions are linked to the central Zn(II) via a μ-l,l azido bridge giving rise to a square pyramidal environment around the Cu(II) ions and consequently the structure becomes linear. These two species can be considered as “linear-bent” isomers. EPR spectra and ESI mass spectra show that the two isomers are identical in solution. The DFT calculation reveals that the energy of 1A is 7.06 kcal mol−1 higher than that of 1B. The existence of both isomers in the solid state suggests that crystal packing interactions in 1A are more efficient and probably compensate for the difference in energy.