In this contribution, we report the synthesis of an imine-based soft 2D covalent organic framework (S-COF) with compacted honeycomb topology via inveterately selecting a helically folded ditopic flexible linker and a trigonal building block. In contrast to various topological structures of rigid monomer-based COFs (R-COFs) reported so far, owing to the presence of flexible skeleton S-COF can spontaneously form a compacted and nonporous topological structure via intramolecular π stacking of presupposed honeycomb-like topology. Such S-COFs with a compacted honeycomb topology have neither been proposed theoretically nor been achieved experimentally. The compacted topological structure of 2D S-COF was clearly characterized by transmission electron microscopy (TEM), atomic force microscopy (AFM), powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), Fourier-transform infrared spectroscopy (FT-IR), and circular dichroism (CD) measurements. This study opens a new window to the development of S-COFs and will significantly expand the scope of COF materials.