We report herein a new microporous neutral three-dimensional (3D) metal–organic framework [Cu₂(L)(DMF)(H₂O)]·guest (1·guest) composed of copper paddle-wheel and flexible tetracarboxylic acid linkers (DMF = N,N-dimethylformamide, H₄L = tetrakis[(6-carboxynaphthoxy)methyl]methane). Surprisingly, this MOF with neutral cavities can not only extract pure quercetin (QT) but also convert it into Cu–QT during the desorption process. It has been well characterized by UV-vis, IR, ESI-MS and TEM-EDS studies. Moreover, it can efficiently extract natural product QT from fresh QT-rich onion juice and rapidly convert it into Cu–QT with a relatively high conversion rate.