A series of 2D/2D MoS2/Bi2WO6 S-scheme heterojunctions consisting of ultrathin MoS2 nanosheets (MS, 1.6 nm) and ultrathin Bi2WO6 nanosheets (BWO, 1.5 nm) were developed for photocatalytic degradation of ciprofloxacin. The samples with 5 % mass ratio of MS (5 %MS/BWO) exhibits the almost complete degradation of ciprofloxacin (≈100 %) under visible light. It is evidenced that the formation of S-scheme heterojunction with close interfacial interaction facilitates the photoinduced carrier separation and the generation of surface acid sites. The activation of ciprofloxacin molecules is realized through the coordinately interaction of C-N and C=O with the surface W sites. Moreover, the OVs in BWO side is a convenient pathway for activated of O2, embodying in the generation of •O2− and •OH under visible light over photocatalyst. Such an association of charge transfer mechanism with coordination activation shows the enhanced photocatalytic performance toward ciprofloxacin. This work provides a motivation which designs an S-scheme heterojunction photocatalyst with the ability to activate the specific group in molecules to comprehend the degradation of antibiotics.