In order to study the remediation of complex wastewater from the groundwater polluted by the electrolytic manganese slag field, the biochar made from pomelo peel was used as the immobilized carrier for the strain Acinetobacter baumannii AL-6 (MBC), and the strain biochar coupling system (MBC) was obtained. The comprehensive treatment performance of the coupling system for composite wastewater containing manganese, ammonia nitrogen and high calcium and magnesium ions was investigated, and a Sequential Batch Reactor (SBR) was constructed to explore its application potential in wastewater treatment. The experimental results showed that MBC removed 98.46% of manganese within 48 h. Compared with two independent experimental groups (biochar group and strain AL-6 group), MBC had an excellent synergistic effect on the removal of manganese and the average removal rate of manganese was 15.87 mg/(L?h), 1.09 times of that of the strain AL-6 and 14.33 times of that of the biochar group. In addition, MBC had a maximum removal rate of 71.92% for ammonia nitrogen, and also had a certain removal effect for calcium and magnesium ions, with removal rates of 41.46% and 26.95%, respectively. In the SBR, 90.1% of manganese and 85.44% of ammonia nitrogen were removed. The results show that immobilized biochar of strain AL-6 made from pomelo peel has great potential and can be used to treat wastewater polluted by electrolytic manganese slag.