Naringin (NRG), known as an important natural flavoniod compounds, exhibits excellent phamaceutical value and clinical application prospect. However, the main obstacle to the isolation and purification of NRG is the low concentration and complexity of the extraction system. Herein, a new kind of hierarchical porous metal–organic frameworks (MOFs) based molecularly imprinted membranes (PBMMA-MIMs) for the specific separation of NRG. The prepared PBMMA-MIMs showed the fast adsorption kinetics (within 120 min). Moreover, the abundant boronic acid imprinted recognition sits and hydrophilic hierarchical porous MOFs improved the adsorption capacity (the maximum adsorption amounts 57.39 μmol/g) and exhibited selective NRG adsorption (imprinting factor 2.31) with efficiency over 91.69 % after seven adsorption–desorption cycles. In addition, the coarse NRG could be effectively extracted to a promising purity of 93.13 % via PBMMA-MIMs. This study provides new insights into the design molecularly imprinted membranes via environmentally friendly synthesis route for the preparation for enriching high-value flavoniods, achieving efficient purification rate of agricultural wastes for pollution control, and promoting the sustainable reuse in complex agricultural wastewater.