Sponge is widely used in our daily life as a low-cost and easily available material. Its three-dimensional (3D) porous structure is particularly suitable for the application of membrane-based separation. Herein, we report an antibacterial, high-flux and 3D porous molecularly imprinted nanocomposite sponge membranes (Emodin-MIS) based on sponge for cross-flow filtration of emodin from analogues (aloe-emodin and physcion). A GO/Ag/KH570 modification strategy was implemented to (i) provide 'active secondary platforms', (ii) increase the antibacterial property, and (iii) facilitate the fixation of molecularly imprinted polymers. Base on formation of 'emodin-recognition sites', optimal selectivity of emodin/aloe-emodin (1.61) and emodin/physcion (1.70) in static adsorption, as well as aloe-emodin/emodin (7.66-3.93) and physcion/emodin (10.00-4.68) in cross-flow filtration, were achieved on Emodin-MIS with the imprinting factor of 3.28. Langmuir isothermal model and pseudo-second-order kinetic model best fitted rebinding data of Emodin-MIS. Specifically, the rebinding capacity of Emodin-MIS was still higher than 85% of initial after 10 regeneration cycles which included an interval of 15 days. This novel-designed Emodin-MIS exhibits superior results for emodin separation in cross-flow filtration and shows promising potentials for wider applications.