A half-conjugate polydentate Salamo-Salen hybrid ligand, H5L, containing two unique N2O2 pockets was first designed so that these metal ions in the complexes appear in different coordination modes. Two heterohexanuclear 3d-s double-helical cluster complexes, [Zn4Ca2L2(μ1-OAc)2(EtOH)2]·2EtOH (1; EtOH = ethanol) and [Zn4Sr2L2(μ2-OAc)2(MeOH)2]·2CH2Cl2 (2; MeOH = methanol), are reported that are formed through the reaction of H5L with zinc(II) and calcium(II) acetate or strontium(II) acetate, respectively. IR spectral analysis of the two complexes showed the existence of monodentate- and bidentate-coordinated acetate ions. The fluorescence properties of the ligand and its two heterohexanuclear complexes were explored in MeOH and water solutions, separately. In addition, theoretical calculations (density functional theory, interaction region indicator, and bond order) were performed to further understand the formation of a single-molecular double helix and the electron distribution characteristics of the two complexes.