A University of Cape Town process coupled with integrated fixed biofilm and activated sludge system was modified by bypass flow strategy (BUCT–IFAS) to enhance nitrogen and phosphorus removal from the wastewater containing insufficient carbon source. This process was operated under different bypass flow ratios (λ were 0, 0.4, 0.5, 0.6 and 0.7, respectively) to investigate the effect of different operational modes on the nitrogen (N) and phosphorus (P) removal efficiency (λ = 0 was noted as common mode, other λ were noted as bypass flow mode), and optimizing the N and P removal efficiency by altering the λ. Results showed that the best total nitrogen (TN) and total phosphorus (TP) removal performances were achieved at λ of 0.6, the effluent TN and TP averaged 14.0 and 0.4 mg/L meeting discharge standard (TN < 15 mg/L, TP < 0.5 mg/L). Correspondingly, the TN and TP removal efficiencies were 70% and 94%, respectively, which were 24 and 41% higher than those at λ of 0. In addition, the denitrification and anoxic P-uptake rates were increased by 23% and 23%, respectively, compared with those at λ of 0. These results demonstrated that the BUCT–IFAS process was an attractive method for enhancing nitrogen and phosphorus removal from wastewater containing insufficient carbon source.