Carbon saving, oxygen consumption reduction and cellular matter production reduction of Modified University of Cape Town (MUCT) process under different nitrate-nitrogen concentration in the main anoxic section was studied. This was investigated by material balance analysis, biochemical reaction process and its metrology of ordinary heterotrophic bacteria, denitrifying bacteria, nitrifying bacteria and phosphorus-accumulating bacteria. The flow and distribution of carbon, nitrogen, and oxygen in the MUCT, and the influence of the regulation of the c(NO3) on the carbon source, cellular matter production, and oxygen consumption of the process were explained in detail. In the programmable logic controller (PLC) automatic control system, the circulating flow rate of nitrate was set as the controlled variable. Adopting the feedback control structure, c(NO3) was altered at 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5 and 4.0mgㆍL-1, respectively. In this experimental study, the quality of influent and other operation design parameters remained unchanged. The results showed that the effluent quality was at its best when c(NO3) was controlled at 2.0- 4.0mg/L. Again, the distribution of chemical oxygen demand (COD) in the anaerobic section was between phosphorus- accumulating bacteria, common heterotrophic bacteria and denitrifying bacteria, and the distribution was related to c(NO3). Due to this phenomenon, the distribution of nitrate-nitrogen between denitrifying bacteria and denitrifying phosphorus-accumulating bacteria, and poly-hydroxy alkanoates (PHA) between denitrifying phosphorus-accumulating bacteria and aerobic phosphorus-accumulating bacteria was changed. Carbon source of 110.0 kg acetic acid/103m3 sewage was saved, while the cell material output was reduced by 37.5%, and the oxygen consumption of 51.1 kg O2/ 103m3 sewage was reduced. In the MUCT process, the regulation of c(NO3) enhanced the denitrifying phosphorus uptake performance of the main anoxic section and obtained good carbon source savings, reduction of cellular matter production, and reduction of oxygen consumption.