In this work, modified magnetic graphene quantum dots with molecularly imprinted polymer coating (Fe3O4@GQDs/MIP) through the self-assembly reaction of APTES (functional monomer), TEOS (cross-linker) and quercetin (template) molecules as a low-cost new green adsorbent with high selectivity and sensitivity for easy evaluation of quercetin medicinal compound using the quenching effect of quercetin on the fluorescence emission intensity of graphene quantum dots (GQDs) were synthesized. The morphology and composition of GQDs, magnetic graphene quantum dots (Fe3O4@GQDs) and Fe3O4@GQDs/MIP by Fourier transform infrared spectroscopy (FT-IR), vibrating sample magnetometer (VSM), scanning electron microscopy (SEM) and energydispersive X-ray spectroscopy (EDAX) techniques were determined. The regular and uniform distribution of spherical nanoparticles of Fe3O4@GQDs/MIP was well observed by SEM imagings. In the next part of this project, the effective parameters in the process of measuring quercetin such as concentration of adsorbent, pH and contact time were investigated, that the optimal values of concentration of adsorbent 0.6 mg mL− 1 , pH 8.0 and contact time 10 min were obtained. In the optimized conditions, quercetin with a linear range of 5–220 ng mL− 1 with detection limit of 0.54 ng mL− 1 and recoveries of 97.61–102.11(%) and repeatability of 1.18–3.71(%) in real samples of green tea, cumin and thyme was successfully measured and detected.