A molecularly imprinted membrane (MIM) was prepared in aqueous media using chitosan (CS) as a functional polymer, naringin (NG) as a template molecule by phase-inversion technique. The morphologies of the MIM before and after modification with the porogen (PEG) were observed by SEM. The imprinted membrane showed an excellent performance when sulfuric acid was used as a cross-linking agent at the mass ratio of CS:NG = 15:1. The FT-IR spectra confirmed that the formation of hydrogen bond between functional polymer and template molecules. The NG-CS MIM was used to separate NG from neohesperidin/NG in the aqueous media, and the highest permeation percentage was 11.16% for 8 h.