Abstract: Acid mine water (AMD) can cause many environmental and social problems. The high sulfate ion content in AMD is one of the key factors contributing to contamination. Microbial electrolytic cell (MEC) is an electrically mediated microbial electrochemical technology. In explore the mechanism of the effect of MEC on AMD-containing sulfate, the construction of microbial sulfur removal system (MEC-CS) and CS system with SO₄²⁻ removal rate as the target were discussed. Hash water analyzer (DR2600), ion chromatograph (TIS), and pyrophosphate sequencing were applied to analyze the desulfurization efficiency, the activity of electro-microorganisms on electrodes, and the evolution pattern of intermediate key ion products in both treatment systems. The results show that: The maximum sulfate removal rate in the MEC-CS system was 62.6%, which was 33.9% higher than that of the conventional CS system (28.7%), it indicates that the desulfurization capacity and AMD processing capacity are effectively improved; Sequencing results showed that Desulfovibrio and Desulfobacterium were most enriched in the cathode electrode, this indicates that a certain voltage promotes the activity of sulfate-reducing bacteria and facilitates the desulfurization capacity. In addition, the abundance of various SRBs involved in sulfate reduction was high, and MEC significantly enhanced the hydrogenase activity of SRBs, making them more capable of reduction; MEC-CS has a higher concentration of key intermediate ions (SO₄²⁻ ions, S²⁻ ions, total iron, etc.) realized in the reaction process and a higher conversion rate compared to the CS system. Electrogenic bacteria in the MEC-CS system were less frequently detected in the CS system. MEC enhances the efficiency of sulphuric acid removal by facilitating electron transfer in the microbial desulphurization process, and the method also enables the removal of heavy metal ions such as iron and the recovery of purer minerals. Thus, it provides a new idea for the industrialization and economization of the bioelectric desulfurization process.