In this paper, a study was conducted on the effect of polyhydroxyalkanoates (PHA) and glycogen transformations on biologic nitrogen and phosphorus removal in low dissolved oxygen (DO) systems. Two laboratory-scale sequencing batch reactors (SBR1 and SBR2) were operating with anaerobic/aerobic (low DO, 0.15–0.45 mg·L ) configurations, which cultured a propionic to acetic acid ratio (molar carbon ratio) of 1.0 and 2.0, respectively. Fewer poly-3-hydroxybutyrate (PHB), total PHA, and glycogen transformations were observed with the increase of propionic/acetic acid, along with more poly-3-hydroxyvalerate (PHV) and poly-3-hydroxy-2-methyvalerate (PH2MV) shifts. The total nitrogen (TN) removal efficiency was 68% and 82% in SBR1 and SBR2, respectively. In the two SBRs, the soluble ortho-phosphate (SOP) removal efficiency was 94% and 99%, and the average sludge polyphosphate (poly-P) content (g·g-MLVSS ) was 8.3% and 10.2%, respectively. Thus, the propionic to acetic acid ratio of the influent greatly influenced the PHA form and quantity, glycogen transformation, and poly-P contained in activated sludge and further determined TN and SOP removal efficiency. Moreover, significant correlations between the SOP removal rate and the (PHV+ PH2MV)/PHA ratio were observed ( >0.99). Accordingly, PHA and glycogen transformations should be taken into account as key components for optimizing anaerobic/aerobic (low DO) biologic nitrogen and phosphorus removal systems.