The synthesis of graphdiyne with an ordered internal structure is highly attractive for its various scientific and application investigations. We reported herein a rational method to fabricate a graphdiyne analogue with the help of supramolecular chemistry. The introduction of π-π/CH-π interactions controlled the conformations of the precursors and afforded multilayer graphdiyne analogue Ben-GDY through the wet chemical method. The in-plane periodicity of the multilayer Ben-GDY was corroborated by transmission electron microscopy and selected area electron diffraction, which showed a pattern well matched with ABC-style stacking.