The variability in industrial production often generates wastewater with an unstable carbon-to-sulfur ratio, challenging the concurrent removal of sulfate and organic compounds. Three-dimensional biofilm electrode reactor (3D-BER) technology offers a promising solution, compatible with both autotrophic and heterotrophic sulfate reduction. In this study, four up-flow 3D-BERs with gradient current levels were operated for nearly 400 days to treat simulated high-concentration sulfate wastewater. The effects of current intensity, hydraulic retention time (HRT), and influent carbon-to-sulfur ratio on sulfate and organic removal were investigated. The composition and functions of microbial communities were analyzed by metagenomic sequencing. The synergistic mechanism between heterotrophic and autotrophic sulfate reduction was examined by delineating their individual contributions to sulfate removal. Under optimized conditions (HRT 60 h, influent carbon-to-sulfur ratio of 1.7, and current intensity of 50 mA), the highest removal efficiencies for SO42- and COD reached 70.47 % and 85.58 %, respectively. Elevated current intensity increased the abundances of Desulfuromonadaceae, Desulfovibrionaceae and Methanobacteriaceae, while decreasing Anaerolineaceae and Geobacteraceae. Key genes involved in carbon fixation and hydrogen-relied sulfate reduction showed lower abundances at high current levels, whereas genes for direct electron uptake from the electrode were more abundant. Batch experiments demonstrated a synergistic effect between autotrophic and heterotrophic sulfate reduction, most pronounced at 50 mA. Our work successfully regulates electron donors for microbial reduction of high-concentration sulfate in 3D-BERs by manipulating current intensity, providing new insights into the application of bioelectrochemical technology for complex industrial wastewater treatment.