Laboratory experiments were conducted in a continuous plug-flow anaerobic/aerobic (A/O) process to kinetically investigate the long-term effect of the different carbon sources (i.e., acetate, acetate/propionate, propionate and glucose) on the competition between polyphosphorus accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs). It was found that propionate was more benefit than acetate for PAOs even in the A/O process, and PAOs enriched with acetate were readily able to metabolize propionate without the requirement of adaptation. Glucose gave GAOs metabolic advantage in the PAOs-GAOs competition, which thereby worsened the EBPR performance. Nevertheless, the EBPR capacity could recover by returning carbon to acetate, with the acclimation time of approximately 2-SRTs. This suggests that the varying of carbon can be an effective approach to provide PAOs a competitive advantage over GAOs. Additionally, MLVSS/MLSS could indicate the shift of the microorganism between GAOs and PAOs, but it was not as precise as the biomass-P content.