The complexation of monoalkyl derivatives of ethylenediamine, CnH2n+1+1NHCH2CH2NH2 (n = 8,12,14, 16, and 18), to CuX2 (X- = Cl- or ClO4-) in dilute aqueous dispersions can form stable synthetic bilayer membranes. The aggregate structure and properties of the bilayer membranes have been investigated thoroughly by small-angle X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, electronic reflectance spectroscopy, and differential scanning calorimetry (DSC). The results confirm a strong influence of the counterions on the organized structure of Cu2+-coordinated bilayer membranes. When X- = Cl-, the Cu2+-coordinated headgroups adopt a transconfiguration, which gives a compressed tetrahedral CuN4 environment, and the two tails in the complex take an approximately diagonal position with tilted tail-to-tail packing fashion in bilayer assemblages. When X- = ClO4-, a cis configuration is adopted in the square plane of the Cu2+-coordinated headgroups, and the two tails are located at the same side of the plane and parallel to each other, and the interdigitated chain packing model was adopted in the bilayer membranes. The bilayer membranes formed in these two systems exhibit different appearances and gel-to-liquid crystal phase-transition temperatures due to their different organized structures.