The boronic acid suspended Cr based MIL-100 (MIL-100-B) sorbents have been widely used to separation of cis-diol containing molecules. However, it’s still challenging in fabrication of high performance metal organic frameworks (MOFs) due to its irregular size and low content of functional groups. For improving identification efficiency, the emulsion microreactor were firstly designed to purify MIL-100-B prior to their use. Herein, a highly ordered MOFs-imprinted polymer microsphere was synthesized by O/W Pickering emulsion template, which can highly selective separation of MIL-100-B via the synergistic effect of boronic acid sites and imprinted cavities. The obtained purified H-MIL-100-B exhibited the uniform size and abundant boronic acid groups (B elements ratio up to 27.37 %). The emulsion imprinted microsphere (EIMs) showed the good selectivity towards MIL-100-B. Additionally, the obtained MOF-imprinted microsphere exhibited green, convenient, sustainable separation process towards the purification and recycle of MIL-100-B. The purified MOFs (H-MIL-100-B) were used to specific bind with cis-diol flavoniods naringin (NRG). Satisfactorily, H-MIL-100-B show high adsorption amount (43.69μmol/g at 308 K), fast capture kinetics (160 min), high selectivity and excellent regenerability (up to seven cycles). Remarkably, the purified NRG solutions displayed lasting antibacterial activity against Staphylococcus aureus (S. aureus) with inhibition zone of 13.47 mm. More importantly, the H-MIL-100-B could effectively promote the specific recognition ability of NRG by reducing matrix interference and improving purification efficiency (93.93 %) from complex natural extracts. A high score (0.75) was predicted via analytical GREEnness (AGREE) approaches, demonstrating environmentally friendly and greenness of separation process. The MOFs-imprinted emulsion microspheres possessed dynamic recognition properties towards target MOFs, thus opening new direction for the development of convenient and efficient microreactor for the purification of other functional MOFs.