In this study, pulse discharge technology was adopted for plasma generation. And it can be applied for the degradation of pharmaceutical wastewater. Several typical pharmaceutical, such as sulphadiazine, sulphamethoxazole, sulphadimidine, sulphamilone, norfloxacin, roxithromycin, gentamicin, chloramphenicol and penicillin, were selected to simulate pharmaceutical wastewater. Study on their degradation performance. Magnetic mesoporous silica (MMS) coupled with plasma can considerably increase thepenicillin removal efficiency more 45% than plasma alone. The pulse discharge can generate plasma to collide water molecules to produce the solvent electron, initiate excited species, such as hydroxyl radicals (•OH), superoxide anion radical (O2-•), hydrogen peroxide, ozone (O3) and so on, which contributed to decompose pharmaceutical efficiently. Furthermore, pharmaceutical removal efficiency can reach basically above 99%. The energy consumption in this system was relatively lower than that in other system. Penicillin is selected as the typical representative of organic pollutants in pharmaceutical wastewater. Density Functional Theory (DFT) and Δƒ(r) for nucleophilicity and electrophilicity were used to insight into the penicillin degradation mechanism. The calculation results indicated that the 20 C, 8 N, 9 C, 10 N, 12 C, 14 N, 17 S, 19 C and 7 C atoms were susceptible to be collided to excite by the solvent electron or excited species, resulting in the cleavage of the chemical bonds of penicillin, therefore, decomposing penicillin molecules to remove from wastewater in the catalytic pulse discharge plasma system. Further on, the experimental detection intermediates by UPLC-MS was in good agreement with the theoretical Δƒ(r) results. Thus, the degradation pathways and mechanism of penicillin could be clearly inferred. This study offers some theoretical guidance to purify all kinds of pharmaceutical wastewater, but many factors need to be involved in practical application.