Antibiotics are resistant compounds with low biological degradation that generally cannot be removed by conventional wastewater treatment processes. The use of yolk-shell nanostructures in spinning disc photocatalytic reactor (SDPR) enhances the removal efficiency due to their high surface-to-volume ratio and increased interaction between catalyst particles and reactants. The purpose of this study is to investigate the SDPR equipped to Fe3O4@void@CuO/ZnO yolk-shell thin film nanostructure (FCZ YS) in the presence of visible light illumination in the photocatalytic degradation of amoxicillin (AMX) from aqueous solutions. Stober, co-precipitation, and self-transformation methods were used for the synthesis of FCZ YS thin film nanostructure and the physical and chemical characteristics of the catalyst were analyzed by XRD, VSM,, EDX, FESEM, TEM, AFM, BET, contact angle (CA), and DRS. Then, the effect of different parameters including pH (3–11), initial concentration of AMX (10–50 mg/L), flow rate (10–25 mL/s) and rotational speed (100–400 rpm) at different times in the photocatalytic degradation of AMX were studied. The obtained results indicated that the highest degradation efficiency of 97.6% and constant reaction rate of AMX were obtained under LED visible light illumination and optimal conditions of pH = 5, initial AMX concentration of 30 mg/L, solution flow rate of 15 mL/s, rotational speed of 300 rpm and illumination time of 80 min. The durability and reusability of the nanostructure were tested, that after 5 runs had a suitable degradation rate. Considering the appropriate efficiency of amoxicillin degradation by FCZ YS nanostructure, the use of Fe3O4@void@CuO/ZnO thin film in SDPR is suggested in water and wastewater treatment processes.