The partial nitrification-anammox (PNA) process under intermittent aeration is feasible to treat low-strength ammonium wastewater, but the effect of chemical oxygen demand (COD) on mainstream anammox processes is not fully understood. In this study, PNA process was established for sewage treatment (average ammonium = 59.3 mg-N/L) in a sequencing batch reactor (SBR) with intermittent aeration mode. Influent organic carbon to nitrogen (C/N) ratios were gradually increased (1.1, 1.5, 2.0 and 2.5). With increasing C/N ratios, the total nitrogen (TN) removal efficiency increased steadily from 30.8% to 77.3%. When the C/N ratio increased from 1.1 to 2.0, the improvement of nitrogen removal was attributed to the increase of anammox bacteria, which exponentially increased at the C/N ratios from 1.1 to 1.5. Additionally, nitrate reduction using internal carbon was likely to combine with anammox reaction under intermittent aeration operation, which might further improve the nitrogen removal. Lastly, settleability and particle size of activated sludge were also improved with the elevated C/N ratios, which favored the enrichment of anammox bacteria and facilitated the combination of partial denitrification and anammox. When the C/N ratio was 2.5, TN removal efficiency still increased while the abundance and activity of anammox bacteria remained stable, indicating that influent organic carbon promoted denitrifying bacteria and inhibited anammox bacterial growth rate. Overall, this study demonstrates that influent COD has comprehensive effects on PNA systems and that the influent C/N ratios are suggested to adjust within optimal range to achieve long-term stability.