Advanced oxidation technologies based on hydroxyl radical (•OH) and sulfate radical (SO4-•) are two common types of advanced oxidation technologies, but there are not many reports on the application of advanced oxidation methods in actual wastewater pretreatment. This article compares the pre-treatment performance of Fe2+/H2O2 and Fe2+/Persulfate systems in actual pharmaceutical wastewater, and combines EEM, GC-MS, and toxicity testing results to explore the differences in TOC, COD, and NH3-N removal rates, optimal catalyst dosage, applicable pH range, toxicity of effluent after reaction, and pollutant structure between the two systems. The results indicate that the Fe2+/H2O2 system has a higher pollutant removal rate (TOC: 71.9%, COD: 66.9%, NH3-N: 34.1%), but also requires a higher catalyst (Fe2+) concentration (6.0 g/L), and its effluent exhibits characteristic peaks of aromatic proteins. The Fe2+/Persulfate system has a wider pH range (pH ≈ 3-7) and is more advantageous in treating wastewater containing more cyclic organic compounds, but the effluent contains some sulfur-containing compounds. In addition, toxicity tests have shown that the toxicity reduction effect of the Fe2+/Persulfate system is stronger than that of the Fe2+/H2O2 system.