Three-dimensional sphere covalent organic framework (3D-S-COF) membranes have received increasing attention in the field of oily wastewater and industrial organic matter due to their rich pore structure as well as having many exposed functional group sites. However, the synthesis of conventional imine COF through the Schiff base method, which suffers from the easy hydrolysis under organic solvent conditions. Herein, a novel super-wettable MXene/3D-S-COF composite membrane for oil–water emulsion separation was prepared by depositing MXene nanosheets on oxidized amide COF from the imine COF. The hydroxyl groups of the COF membrane not only improved the water permeability but also formed hydrogen bonds with the MXene layer, which enhanced the interaction and formed the high stability composite membrane. The porous 3D-S-COF and the zigzag MXene layer work synergistically to enable emulsion fluxes up to 240 L·m−2h−1 bar−1 and the separation efficiency is more than 98 %. In addition, the residual mass of the composite membrane remained above 95 % after 10 days of immersion in various solvents, and it also has photocatalytic properties and good resistance to fouling. This study provides a brand new idea for the use of MXene/3D-S-COF based composite membrane for oil–water emulsion separation.