To maximize pollutant removal efficiency with minimal energy consumption, electrochemical process for wastewater treatment should be further conducted. The stepping control of electrochemical process for simultaneous removal of chemical oxygen demand (COD) and ammonia from simulated and actual wastewater with high efficiency and energy saving was studied in this work. Flow rate, initial pH value, Cl− concentration, and applied current density were determined to be the influencing factors for the degradation performance, and analyses of pollutant removal efficiency further revealed that applied current density was the significant parameter in this case. A stepping control system by operating applied current density timely based on the degradation pathway of organic matter and variation of anodic working potential was then proposed; results indicated that 90.9% COD and 100% ammonia could be removed, and energy consumption of 7.6 kWh m−3 was calculated, which was substantially lower than that of the traditional electro-oxidation system (11.7 kWh m−3). Additionally, the developed stepping control system was validated by treating an actual pharmaceutical wastewater, results for which showed that removal efficiencies of 81.7% and 100% were achieved for COD and ammonia, respectively, and energy saving could be up to 37.2%.