Chemical wastewater has a high concentration of toxic and hazardous antibiotic pollutants, which not only devastates the ecological environment and disrupts the ecological balance, but also endangers human health. This research proposed a non-thermal plasma (NTP) combined with a ZnO-Fe3O4 nano-catalyst system to achieve the efficient degradation of ciprofloxacin (CIP) in chemical wastewater. Firstly, ZnO-Fe3O4 composite materials were prepared using hydrothermal method and characterized with scanning electron microscopy (SEM), transmission electron microscope (TEM), X-ray diffractometer (XRD), X-ray photoelectron spectroscopy (XPS), etc. With the sole NTP, NTP/ZnO, and NTP/ZnO-Fe3O4 systems, the removal efficiency of CIP can reach 80.1%, 88.2%, and 99.6%, respectively. The optimal doping amount of Fe3O4 is 14%. Secondly, the capture agent experiment verified that ·OH, ·O2−, and 1O2 all have a certain effect on CIP degradation. Then, liquid chromatography–mass spectrometry (LC-MS) was used to detect the intermediate and speculate its degradation pathway, which mainly included hydroxyl addition, hydroxyl substitution, and piperazine ring destruction. After treatment with the NTP/ZnO-Fe3O4 system, the overall toxicity of the product was reduced. Finally, a cyclic experiment was conducted, and it was found that the prepared ZnO-Fe3O4 catalyst has good reusability. The NTP/ZnO-Fe3O4 was also applied in practical pharmaceutical wastewater treatment and has practical applicability.