In this work, a nanocomposite, Fe3O4/graphene was prepared and characterized. Five profens (including ibuprofen, flurbiprofen, pranoprofen, indoprofen and loxoprofen sodium) were extracted from three environmental water samples by using the synthetic Fe3O4/graphene, followed by simultaneous determination of the enantiomers on a Chiralcel OJ-RH column coupled with a triple quadrupole mass spectrometry. Factors affecting the extraction efficiency, such as amount of adsorbents, solution pH, ionic strength, type and volume of desorption solvent, as well as elution time were thoroughly investigated. Method validation showed high sensitivity with method quantification limits in the range of 8.49–26.3 ng/L. Satisfactory recovery (73.6–90.2%), good intra-day precision (RSD 3.2–9.7%) and inter-day precision (RSD 5.2–10%) were also obtained. Furthermore, possible interactions between analyte and graphene, such as electrostatic attraction, charge-π interaction, hydrophobic interaction and π-π stacking were discussed by combining the experiment results and molecular docking study, which provided a new insight into the adsorption mechanism of graphene.