Functioned covalent organic frameworks (COFs) have attracted tremendous attentions in the separation fields. Nonetheless, the application of COFs sorbents under complex flavoniod separation conditions still confronts many difficulties. Herein, for the fist time, the rod-shaped COFs molecular imprinted polymers (RCOFs-SH@BA-MIPs) with abundant hydrophilic boronate affinity imprinted recognition sites were synthesized. The obtained rod-shaped COFs-MIPs were firstly used to stabilized Pickering HIPEs, which greatly enhanced flavoniod molecules transport in hierarchically porous polymers. Meanwhile, the HPs@RCOFs-SH@BA-MIPs sorbents exhibited the promising contact angle (112.52°) owing to the introduction of hydrophilic boronic acid imprinted recognizing site. The resulting HPs@RCOFs-SH@BA-MIPs sorbents showed excellent adsorption capacity (49.0 µmol g−1) in phosphate acetic acid/water solution (T = 303 K, pH = 8.0, v/v, 9/1) and selectivity (superior to 1.19). At the same time, HPs@RCOFs-SH@BA-MIPs exhibited a fast adsorption kinetics for NRG (180 min). In addition, the HPs@RCOFs-SH@BA-MIPs sorbents showed excellent stability (94.9 %) after six cycles. The effective extraction rate of commercial NRG treatment with HPs@RCOFs-SH@BA-MIPs were as high as 91.0 %. Abundant boronate affinity imprinted recognition sites played an important role in the adsorption of NRG, and emulsion interfacial polymerization strategy avoided the leakage of nanosize-imprinted adsorbents (HPs@RCOFs-SH@BA-MIPs). Finally, the promising experimental results and the convenient synthesis process indicate that HPs@RCOFs-SH@BA-MIPs have great potential for application in specific separation, agricultural environment, chemical engineering and other field.