To address the issue of secondary effluent from fermentation pharmaceutical wastewater exceeding discharge standards, a test was conducted using three-dimensional electrolysis coupled with Fenton treatment to oxidize the wastewater, considering its difficult biodegradability. Through a one-factor test, the effect of different operating conditions on the COD removal rate of wastewater was explored, using kinetic equations to examine the system's reaction rate and the relationship between reactant concentration and change. The results showed that the COD removal rate reached 72.6% when the reaction time was 120 min, the current intensity was 1.50 A, the activated carbon dosage was 20.00 g/L, the H2O2 concentration was 8.00 mmol/L, the initial pH was 3.00, the Fe2+ concentration was 2.00 mmol/L, and the spacing between the plates was 5 cm. It complies with the discharge requirements of the Emission Standards for Water Pollutants in the Fermentation Pharmaceutical Industry and exceeds the Class A standard of the Emission Standards for Pollutants from Urban Wastewater Treatment Plants. The three-dimensional electrolysis coupled Fenton process effectively treats fermented pharmaceutical wastewater secondary effluent in accordance with the three-level kinetic law and attenuation model.