In the literature most of the studies on the effect of pH on enhanced biological phosphorous removal were conducted with the acetate wastewater, and the pH was controlled during the entire anaerobic and aerobic stages. This paper investigated the influence of anaerobic initial pH control, which will be more practical than the entire process pH control strategy, on enhanced biological phosphorus removal from wastewater containing acetic and propionic acids. Typical pH profile showed that both the initial alkaline and acidic pH tended to neutralize due to the consumption of short-chain fatty acid (SCFA) and intracellular pH regulation by polyphosphate accumulating organisms (PAOs). It was observed that the glycogen degradation and polyhydroxyalkanoates (PHA) accumulation decreased with increasing initial pH, which disagreed with previous reports. In the literature the metabolisms of both glycogen and PHA by PAOs in the acetate wastewater were independent of pH. An anaerobic mechanism model was proposed to explain the intra- and extra-cellular pH buffer nature of PAOs, and to address the reasons for increased polyphosphate degradation and decreased PHA synthesis and glycogen degradation at higher pH. The optimal initial pH for higher soluble ortho-phosphorus (SOP) removal efficiency should be controlled between 6.4 and 7.2. This pH control strategy will be easier to use in practice of wastewater treatment plant.