A continuous microbial fuel cell system was constructed treating ammonium/organics rich wastewater. Operational performance of MFC system, mechanisms of ammonium removal, effect of ammonium on organics removal and energy output, C and N balance of anode chamber and microbial community analysis of anode chamber were studied. It was concluded that 0.0914kg/m3d NH4+-N and 5.739kg/m3d COD were removed from anode chamber and simultaneous nitrification and denitrification (SND) occurred in cathode chamber resulting in COD, TN removal rate of 88.53%, 71.35% respectively. Excess ammonium affected energy output and the MFC system reached maximum energy output of 816.8mV and 62.94mW/m3. In anode chamber, Spirochaetes bacterium sp., Methanobacterium formicicum sp. was predominant in bacteria, archaea communities respectively which contributed to wastewater treatment and electricity generation. This study showed the potential for practical application of continuous flow MFC system treating ammonium/organics rich wastewater and achieving electricity generation simultaneously.