Metal-organic frameworks (MOFs) and covalent organic frameworks (COFs) hybrids are novel porous composite materials with potential applications in advanced membrane separations. However, the preparation of defect-free and self-standing separation membranes remains challenging. Here, we report a COF-MOF composite membrane with a sandwich layer structure and a two-dimensional (2D) intergrown nanosheet morphology. This was achieved by inducing the secondary growth of a layer of MOF (ZIF-67) membrane using a two-dimensional COF (TpPa1) membrane as a seed layer and porous support. It is worth noting that a rare ZIF-67 membrane consisting of 2D nanosheets was grown on the TpPa1 porous support. The [TpPa1]-[ZIF-67] membranes exhibited excellent permeance for organic solvents, pure water (95.3 L m−2 h−1 bar−1), with high rejection rates (>97 %) towards dyes larger than 700 Da, while maintaining a low rejection rate for hydrated salt ions (<14 %) and outstanding dye/salt selectivity. The membranes also displayed considerable long-term operational stability and could be easily transferred to other substrates without damaging their integrity. The excellent separation properties achieved through layer-by-layer filtration are mainly due to the sandwich structure and the synergistic effect of the components.