Abstract: Discharge of aquaculture wastewater from large-scale pig farms has become one of the major pollution sources for agricultural non-point sources in China. After the treatment of anaerobic fermentation for aquaculture wastewater, most of the COD is removed, but the concentration of NH4+-N is still very high, leading to the production of biogas slurry with the low ratio of C/N and high strength of ammonia nitrogen. If the concentration of NH4+-N was high beyond the threshold of conventional denitrification microorganisms, the enrichment difficulty with the seriously unbalanced C/N ratio can occur, while, the low organic matter also affects the removal of total nitrogen. Therefore, it is highly demanding to explore a new biological treatment technology that suitable for this kind of biogas slurry, in order to ensure the sustainable development of industrial aquaculture in animal husbandry. In view of the water quality characteristics of oligotrophic and high ammonia nitrogen, a novel process was proposed to combine three-dimensional rotating biological contactor (3D-RBC) and biological contact oxidation (BCO) reactor using the oligotrophic heterotrophic nitrification-aerobic denitrification (HN-AD) mixed bacteria with high tolerance of ammonia nitrogen as microbial inoculants for the treatment of piggery biogas slurry wastewater. The removal efficiency of pollutants was also evaluated in the combination process under the condition of actual biogas slurry. An emphasis was put on the effects of concentration of dissolved oxygen (DO) and C/N ratio on the removal of pollutant during the treatment. A high-throughput sequencing technology was selected to analyze the change of microbial community structure in optimization process of DO and C/N ratio. The results showed that: (1) In the case of actual biogas slurry, the start-up of 3D-RBC and BCO reactors can be completed in 12d and 18d, respectively, when using the HN-AD mixed bacteria as microbial inoculants for the biofilm formation. The removal efficiency of COD, NH4+-N, and TN in the combined process were 94.8%, 95.7% and 80.1%, respectively, and the effluent water quality can reach the level of Class I-B according the national standard GB 18918-2002. (2) During the optimization of DO and C/N ratios in the 3D-RBC reactor, the removal rates of COD, NH4+-N, and TN were reduced by 25.4%, 15.4%, and 15.5%, respectively, particularly after the addition of the bottom exposure. There was no significantly increase in the removal efficiency of COD, NH4+-N, TN, and TP, whereas, the energy consumption of aeration increased in the combination process. The combined process can be especially suitable to treat the biogas slurry with the low C/N ratio and high concentration of nitrogen. The improved C/N ratio can lead to the decrease in the removal rate of TN , while, increase the cost of carbon in the treatment of 3D-RBC. (3) The biodiversity in the 3D-RBC disc biofilm decreased slightly after the addition of bottom exposure, but the variety and abundance of the dominant genus HN-AD decreased significantly, leading to a decrease in the removal efficiency of nitrogen. When C/N=1 and C/N=3, Pseudomonas and Acinetobacter have relatively high abundance, whereas, its abundance decreased significantly while the nitrogen removal efficiency decreased, when C/N increased to 6. The oligotrophic Acinetobacter and Pseudomonas bacteria can serve as the key materials for the efficient removal of nitrogen from actual biogas slurry in the 3D-RBC. It infers that the decrease of C/N ratio can significantly enhance its abundance, and thereby improve the nitrogen removal.