ABSTRACT: Covalent organic frameworks (COFs) with a pore size beyond 5 nm are still rarely seen in this emerging field. Besides obvious complications like the elaborated synthesis of large linkers with sufficient solubility, more subtle challenges regarding large-pore COF synthesis, including pore occlusion and collapse, prevail. Here we present two isoreticular series of large-pore imine COFs with pore sizes up to 5.8 nm and correlate the interlayer interactions with the structure and ther-mal behavior of the COFs. By adjusting interlayer interactions through the incorporation of methoxy groups acting as pore-directing “anchors”, different stacking modes can be accessed, resulting in modified stacking polytypes and, hence, effective pore sizes. A strong correlation between stacking energy towards highly ordered, nearly-eclipsed structures, higher struc-tural integrity during thermal stress, and a novel, thermally induced phase transition of stacking modes in COFs was found, which sheds light on viable design strategies for increased structural control and stability in large-pore COFs. This dataset contains all data from analytical measurements including FT-IR spectra, raw XRD patterns, 1H and 13C ssNMR and lNMR spectra, TGA, N2 sorption isotherms, pore-size distributions, BET plots, SEm and TEM images, quantum-chemically optimized structures, CIFs of the journal article mentioned under the related publication. Open .cif and .xyz files with a visualization software (see http://ww1.iucr.org/iucr-top/cif/), .raw files with WinXPOW, .sp files with PerkinElmer Spectrum software, .mnova files with MestReNova, .fq/.gr/iq/sq files with a text editor, .qps with ASiQwin, and *.pro files with TOPAS.