The slow hydrolysis rate and ammonia inhibition effects significantly limit the performance of anaerobic digestion (AD) of nitrogen rich wastes. An innovative two-stage AD was therefore investigated for chicken manure by combining hyper-thermophilic (70 °C) pretreatment and a anaerobic membrane bioreactor (AnMBR). An in-situ stripping unit was assembled into the AnMBR to remove the ammonium-N, thus alleviating the inhibition effects. Through the 120-day experiment, the hydraulic retention time was optimized at 15 days for AnMBR with a constant retention 4 days for pretreatment. The hydrolysis efficiency and methane yield reached 72.4% and 352 mL-CH4/g-VSin respectively. About 3000 mg/L ammonium-N was removed through stripping, attributing to methane yield increased by 139 mL-CH4/g-VSin and volatile fatty acids decreased by 2683 mg/L compared to the control. No significant fouling was observed for the membrane. Conclusively, the combined two-stage AD process may offer an alternative approach for the treatment of nitrogen rich organic waste.