In the coal chemical industry, the concentrated waters produced by nanofiltration and reverse osmosis are usually evaporated and crystallized. During the evaporation crystallization process, high COD levels can lead to problems such as the entrainment of liquid droplets and excessive amounts of mother liquor. Therefore, there is an urgent need to develop efficient, stable, and engineering-applicable organic matter degradation technologies before the evaporation crystallization process. In this study, Ti-ENTA/SnO2-Sb and GF-5 were combined as cathodes to form an electrochemical flow-through oxidation system to treat nanofiltration concentrate (NFCs) and reverse osmosis concentrate (ROCs). The experimental results show that within the current density range of 10–20mA·cm−2, the chemical oxygen demand (COD) removal rates of NFCs and ROCs are 55.3%–85.2% and 49.9%–93.6%, respectively. And the oxidation system can be used stably for a long time, fully meeting the practical application needs. In addition, this article further analyzed the effects of current density, initial organic matter concentration, pH value, and electrode spacing on COD removal. The results indicate that the COD removal efficiency is mainly affected by current density and initial organic matter concentration. Finally, a comprehensive comparison was made on the efficiency and cost of various advanced oxidation technologies in treating wastewater. The results indicate that the electrochemical flow-through oxidation system has significant cost advantages. The cost of processing NFCs and ROCs per cubic meter is $0.96 and $1.23, respectively. These findings indicate that the electrochemical flow-through oxidation system proposed is an advanced oxidation technology with economic benefits and practical application prospects.