This study investigated the interaction processes of ciprofloxacin (CIP) with graphene oxide (GO) and reduced GO (rGO) in presence of montmorillonite (Mont) in simulated gastrointestinal fluids. The order of CIP adsorption affinity was rGO+Mont > GO+Mont > rGO+Mont+pepsin > rGO > GO+Mont+pepsin > Mont > Mont+pepsin > GO > rGO+pepsin > GO+pepsin in simulated gastric fluid. Mont enhanced the adsorption of CIP on GO and rGO due to hydrated Si species coating on GO and rGO in the simulated gastric fluid. Meanwhile, π-π interaction between CIP and graphene caused the great shift of two cyclopropyl CH2 and one cyclopropyl in CIP molecules. And GO, rGO, and Mont interacted mainly with CIP by COOH groups. CIP and pepsin molecules could intercalate and increase the basal spacing of Mont as well. After the various interaction systems of adsorbent-adsorbate transferring to the simulated intestinal fluid, CIP was continuously adsorbed by GO and rGO. In addition, adsorbed CIP was released from Mont into the solution through electrostatic repulsion. The decrease ratio of CIP was the lowest in the GO/rGO+Mont+pepsin systems. Therefore, the mixture of Mont and GO/rGO decreased the CIP concentration in gastrointestinal fluid to weaken further antibiotic activity of CIP.