Hydrogel-based imprinted materials with specific-recognition and ultrafast transport have been considered as one of the most promising sorbents in the selective separation fields. Nonetheless, the traditional hydrogel imprinted sorbents still facing the low-level interfacial consistency between substrate polymer and imprinted sites, unordered arrangement and easy agglomeration of recognizing sites on hydrogel matrix, causing poor selectivity of specific molecular transport. For the first time, the one-step RAFT Pickering HIPEs emulsion imprinted methods were designed to fabricate porous hydrophilic boronate affinity imprinted hydrogels (POH-BA-MIPs) for the specific separation and purification of Naringin (NRG). As expected, the novel RAFT solid emulsifier can not only enhance the emulsion stability and mechanical performance of the hydrogel, but also introduce the self-initiating function. Benefiting from the hydrogel’s porous structure and the highly accessible and uniform imprinted sites via Pickering emulsion template, the POH-BA-MIPs exhibited strong binding affinity and selectivity to the targeted molecules. The maximum equilibrium adsorption capacity of POH-BA-MIPs were 53.27 µmol g−1 at 308 K within 360 min. The kinetic nonlinear pseudo-second-order model (R2 = 0.997) can well explain the adsorption kinetic than pseudo-first-order model (R2 = 0.986), indicating that chemisorption is mainly the rate-limiting step. Besides, the adsorption amounts of POH-BA-MIPs were 3.74 times higher than that of non-imprinted adsorbents (POH-BA-NIPs). After six consecutive adsorption–desorption cycles, the obtained POH-BA-MIPs demonstrated considerable reusability, retaining 91.28 % of the initial adsorption capacity. Meanwhile, the coarse NRG products can be effectively purified to 93.16 %. The obtained purified NRG had better antibacterial performance against Staphylococcus aureus. This work provides a novel strategy for constructing porous boronate affinity imprinted hydrogels for specific capture of targeted flavonoid molecules, which exhibited broad practical application potential.