Ionic liquid (IL)-based aqueous two-phase systems (ATPSs) are formed by the phase separation of aqueous mixture of ILs. Owing to their unique interfacial properties and stable interfacial zone, IL-based ATPSs can work as a promising confined space for membrane processing. Herein, for the first time, we proposed the thermoresponsive IL-based ATPSs as a platform for synthesizing covalent organic framework (COF) membranes. Upon the formation of aqueous biphasic interface at a corresponding temperature, the monomers and catalysts were separately dispersed in the IL-rich phase and water-rich phase. Due to the high viscosity of IL-rich phase and hydrogen bonding interactions in water-rich phase, the diffusion of both aldehyde and amine monomers could be controlled simultaneously and react within the aqueous biphasic interface zone. By optimizing the interfacial properties, the tight and crystalline COF membranes can be achieved with ultrahigh solvent flux and exceptional dye retention performance (>98.0%). For comparison, the homogeneous IL solution realized by temperature without affecting the integrity of the biphasic system was also applied as the medium for COF synthesis and only COF powders with low crystallinity can be obtained. As the pioneering exploitation to fabricate COF membrane at the IL-based aqueous biphasic interface, this work would supply a guiding direction for the green membrane processing strategy.