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• An innovative emulsion interfacial assembly imprinted strategy was designed. • The optimized adsorbent has excellent biocompatibility and mechanical ability. • Hyperbranched imprinted sites facilitate NRG adsorption at multicomponent extract. • The outstanding adsorption selectivity in practical natural products can be enabled. Hydrogel-based molecular imprinted materials have attracted much attention in separation science and technology. However, traditional hydrogel imprinting sorbents face the limited number of imprinting sites, resulting in low adsorption capacity. Herein, a novel hyperbranched boronate affinity imprinted hydrogel (APOH-BA-MIPs) was prepared based on emulsion microreactors for the specific separation of flavoniods. Interestingly, the new Pickering particles (CNCs@GMA@SH-A-CD) with hyperbranched anchor groups and suitable hydrophilic properties were fabricated, which significantly grafted the specific recognizing sites. Meanwhile, the cellulose nanocrystals (CNCs) and cyclodextrins (CDs) composite can effectively enhance the emulsion stability. The addition of functioned CNCs solid emulsifier would effectively enhance the mechanical stability of micro-nano imprinting assembly sorbents during the adsorption process. The mechanical properties of the resulting APOH-BA-MIPs were also improved (Young's moduli 1.73 MPa). The results of adsorption experiments of APOH-BA-MIPs show fast adsorption kinetics (300 min) for NRG under pH = 7.4. The APOH-BA-MIPs still exhibited a significant adsorption capacity (56.03 μmol g−1 at 308 K) for NRG compared to other structural analogues, such as CC, RT, QRCT, ARS and LTL. The imprinting factor (IF) of 3.24 was observed for APOH-BA-MIPs compared to their non-imprinted counterpart. The high affinity site number of APOH-BA-MIPs were calculated to be as high as 53.11 μmol g−1. The regeneration performance of APOH-BA-MIPs still remained at 93.75 % after seven adsorption–desorption cycles. Additionally, the purity can be extracted from agricultural waste pomelo peel to 91.37 %. The purified NRG exhibited excellent antibacterial properties against Staphylococcus aureus. This work provides a new strategy for the fabrication of micr-nano imprinted sorbents with abundant and uniform recognition sites for specific capture flavonoid molecules from agricultural waste. [ABSTRACT FROM AUTHOR]