Quercetin, a bioflavonoid with significant biological activities, is beneficial for health. Herein, a pioneering molecularly imprinted electrochemical sensor utilizing an MXene/CuFe2O4 magnetic nanosphere hybrid was developed for the first time to detect quercetin ultra-sensitively. CuFe2O4 nanospheres (average 189 nm) were synthesized and combined with MXene sheets, then electrostatically deposited onto a magnetic carbon paste electrode. A functional monomer was then electropolymerized onto this hybrid-modified electrode to form an imprinted polymeric layer, tailored for quercetin binding. Characterizations confirmed the morphological and magnetic properties of the materials. The sensor’s response factors were optimized, achieving a low detection limit of 1.6 nM and two linear ranges (0.005–0.7 μM and 0.7–10 μM). The sensor showed excellent stability, repeatability, reproducibility, and selectivity, and was successfully used to quantify quercetin in dietary supplements.