Graphdiyne (GDY) multilayers show stacking-style-dependent physical properties; thus, controlling the stacking style of nanostructures is crucial for utilizing their electrical, optical, and transport properties in electro-optical devices. Herein, we report the assemblies of nanographdiynes decorated with substituents with different steric hindrances to adjust the stacking style. We show that the π-stacked aggregates were influenced by peripheral substituents and the substrate. Steric hexaterphenyl-substituted nanoGDY scaffolds led to dimer structures stacked in the AB-3 configuration with a twist angle of 26.01° or the AB-1 configuration with an in-plane shift along one diyne link. With the interval replacement of steric substituents with long C12 alkyl chains, nanoGDYs were stacked in the AB-2 configuration to decrease the steric congestion, eventually leading to one-dimensional (1D) nanofibrous aggregates. Self-assembly in the presence of substrates can result in ABC-stacked nanoGDYs, which endowed us with the possibility of using nanoGDY as the template for GDY growth in a homogeneous reaction. High-resolution transmission electron microscopy (HRTEM), powder X-ray diffraction (PXRD), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and near-infrared-ultraviolet-visible (NIR-UV-vis) absorption spectroscopy indicate that the crystalline GDY prepared in this way is a 1.18 eV bandgap semiconductor.