Ammonia nitrogen and manganese contained in the leachate of electrolytic manganese residue are causing serious damage to the ecological environment. In this study, anaerobic/oxic (A/O) process as a biological method to achieve simultaneous removal of nitrogen and manganese produced during the actual production of manganese. Results indicated that after 137 d of operation, the system achieved 96.73 ± 1.25%, 98.42 ± 0.60%, 96.97 ± 0.19%, and 100% removal of Mn(II), NH4+-N, TN, and chemical oxygen demand (COD), respectively. Extracellular polymeric substances (EPS) secreted by microorganisms was converted to carbon source to promote denitrification. Scanning electron microscopy (SEM) showed that Mn(II) formed manganese crystals in the process of complete reflection with sludge, acting as electron donor to achieve simultaneous removal of nitrogen and manganese, and removal of Mn(II) was found by X-ray photoelectron spectroscopy (XPS) through redox and valence changes. 16S rRNA indicated that Proteobacteria, Deinococcus-Thermus, Bacteroidete, and Firmicutes were involved in the process of removal nitrogen and manganese. The presence of Limnobacter allowed a more stable accumulation of NO2−-N in reactor, thus achieving shortcut nitrification-denitrification, and Flavihumibacter promoted the secretion of EPS. Collectively, the study reveals that the interaction of autotrophic denitrifying bacteria (Chryseolinea), heterotrophic denitrifying bacteria (Fusibacter, Thauera), and manganese-oxidizing bacteria (Pseudaminobacter, Bacillus, Pedomicrobium, Aeromonasr) achieved simultaneously removal of nitrogen and manganese from the reactor shortcut nitrification-denitrification. This study provides a new insight for the treatment of electrolytic manganese residue leachate produced in the process of manganese production.