Molecularly imprinted membranes have superior selective separation capacity, rebinding capacity, and flux due to their microporous substrates and tightly packed molecularly imprinted polymers. In current study, artemisinin (Ars), the most effective antimalarial drug, is used as template molecule. The permeation-selectivity wooden membranes based on Ars-imprinted nanocages designed by metal organic framework@carbon nitride self-assembly process (MDWMs) has been successfully prepared: (i) based on three-dimensional mesoporous basswood membranes, dopamine-based auto-polymerization process was developed on basswood to for harvest the first layer imprinting and secondary reaction platform. (ii) The two-dimensional sheet carbon nitride modified by metal-organic framework is stably loaded on the surface of the polydopamine-modified basswood membrane, providing a rich irregular point array structure for the formation of recognition sites. Based on elaborate designs and optimizations, selectivity, rebinding capabilities, and flux are enhanced on the developed MDWMs (βAre/Ars = 6.49, βAru/Ars = 4.22, βDH-Ars/Ars = 7.42), and high regeneration rate (>94% after 10 cycles) indicates that MDWMs have superior selectivity and stability. The MDWMs and preparation strategies developed here will provide a completely new design methodology for subsequent selective separation of Ars.