Biological nutrient removal was investigated in a combined modified University of Cape Town and membrane bioreactor system. When the influent nutrient mass ratio (COD/TN/TP) was 28.5/5.1/1 to 28.5/7.2/1, average removal efficiencies of COD, TN and TP were 90%, 81.6%, 75.2%. Obvious denitrifying phosphorus removal occurred with C/N ratio 3.98. When nitrite was the main electron acceptor, the ratio of denitrifying phosphate uptake to the total phosphate uptake were 99.8% and the sludge yield was 0.28kg VSS/kg COD; when nitrate was the main electron acceptor, the ratio was 92% and the yield was 0.32kg VSS/kg COD. In case of nitrite, the system not only kept TP and TN removal at 89.1% and 82.2%, but also ensured less sludge production. Batch tests showed that the proportion of denitrifying phosphorus-accumulating organisms in the total phosphorus-accumulating organisms in the system was higher than 80%.