In an electrochemical reactor made by the authors, the degradation of simulated methyl orange wastewater was experimentally studied by using a diaphragm system with an anode and cathode coaction electrochemical method. Response surface methodology was used to optimize the one-factor test results. The optimum condition was that when the voltage was 20.56 V, the distance between the plates was 4.4 cm, and the aeration rate was 2.21 L/min. The order of influence of each factor was as follows: voltage> distance between electrodes> aeration rate. The two most influential factors were the voltage and aeration rate. Under optimal conditions, the decolorization rate of methyl orange in the cathode chamber reached 90.81%, and in the anode chamber, it was 98.75%. At the same time, the energy expenditure of the diaphragm system during electrolysis is analyzed. UV-visible absorption spectroscopy showed that methyl orange experienced both molecular structure degradation and mineralization during the electrolysis process. The decolorization effect in the anode chamber was better than that in the cathode chamber, but the degree of mineralization of methyl orange in the cathode chamber was better than that in the anode chamber.