To investigate the effect of sulfur–sulfur and metal–ligand coordination on the molecular structure and morphology of self-assembled nanostructures, metal-free 2,3,9,10,16,17,23,24-octakis(isopropylthio)phthalocyanine H2Pc(β-SC3H7)8 (1) and its copper and lead congeners CuPc(β-SC3H7)8 (2) and PbPc(β-SC3H7)8 (3) are synthesized and fabricated into organic nanostructures by a phase-transfer method. The self-assembly properties are investigated by electronic absorption and Fourier transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). Experimental results reveal different molecular packing modes in these aggregates, which in turn result in self-assembled nanostructures with different morphologies ranging from nanobelts for 1 through nanoribbons for 2 to cluster nanoflowers for 3. Intermolecular π–π and sulfur–sulfur interactions between metal-free phthalocyanine 1 lead to the formation of nanobelts. The additional CuS coordination bond between the central copper ion of 2 and the sulfur atom of the adjacent molecule of 2 in cooperation with the intermolecular π–π stacking interaction increases the intermolecular interaction, and results in the formation of long nanoribbons for 2. In contrast to compounds 1 and 2, the special molecular structure of complex 3, together with the intermolecular π–π stacking interaction and additional PbS coordination bond, induces the formation of Pb-connected pseudo-double-deckers during the self-assembly process, which in turn further self-assemble into cluster nanoflowers. In addition, good semiconducting properties of the nanostructures fabricated from phthalocyanine derivatives 1–3 were also revealed by I–V measurements.