A self-inclusion layered discrete CuII complex was synthesized through Cu(NO3)2·2.5H2O and PPz [PPz = trans-2-(2-phenylethenyl)pyrazine]. The single crystal revealed crystallized in the monoclinic C2/c space group, while it contains PPz organic layers and discrete CuII complex layers in turn, integrated formula as [Cu(PPz)2(NO3)2·0.35H2O][PPz]2. In the complex layers, the CuII ions coordinate to the PPz ligands as well as disordered nitrate anions and water molecules. It exists weak C–H⋯π interactions between C(sp2)–H and CPh or CPz (centroid of the phenyl ring or pyrazinyl). Due to the increase of the π⋯acidity of the pyrazinyl rings caused by coordination of CuII ions and N atoms of pyrazinyl rings, the anion⋯π(CPz) binding ability has also been strengthened. Two uncoordinated free ligands PPz act as linkers between discrete CuII complex layers. The weak C–H⋯π and anion⋯π interactions engendered the formation of the crystalline framework. The geometries and frontier molecular orbitals (FMOs) of the complexes were performed with DFT method at B3LYP/6-311++G∗∗ level. The calculated results give a good explanation of the weak interactions.Graphical abstractA self-inclusion layered discrete CuII complex was synthesized through Cu(NO3)2·2.5H2O and PPz [PPz = trans-2-(2-phenylethenyl)pyrazine]. The C−H⋯N/O/C hydrogen bonds, C−H⋯π interactions, and especially anion⋯π interactions, result in the formation of the crystalline framework. The structure was studied by FTIR, elemental analysis, single crystal, thermal analysis and density functional theoretical method at B3LYP/6-311++G∗∗ level.Highlights► We synthesized a self-inclusion CuII–PPz complex with lamellar organic hybrid architecture. ► The noncovalent bonds (C–H⋯π, anion⋯π, C–H⋯N/C) established the complex structure. ► Theoretical results give a good explanation of the week interaction.