Nitrous oxide (N2O) is an important greenhouse gas and a dominant ozone-depleting substance. Nitrification in the activated sludge process (ASP) is an important N2O emission source. This study demonstrated that a short-term low dissolved oxygen (DO) increased the N2O emissions by six times, while long-term low DO operation decreased the N2O emissions by 54% (P < 0.01). Under long-term low DO, the ammonia oxidizer abundance in the ASP increased significantly, and thus, complete nitrification was recovered and no NH3 or nitrite accumulated. Moreover, long-term low DO decreased the abundance of ammonia-oxidizing bacteria (AOB) by 28%, while increased the abundance of ammonia-oxidizing archaea (AOA) by 507%, mainly due to their higher oxygen affinity. As a result, AOA outnumbered AOB with the AOA/AOB amoA gene ratio increasing to 19.5 under long-term low DO. The efficient nitrification and decreased AOB abundance might not increase N2O production via AOB under long-term low DO conditions. The enriched AOA could decrease the N2O emissions because they were reported to lack canonical nitric oxide (NO) reductase genes that convert NO to N2O. Probably because of AOA enrichment, the positive and significant (P = 0.02) correlation of N2O emission and nitrite concentration became insignificant (P = 0.332) after 80 days of low DO operation. Therefore, ASPs can be operated with low DO and extended sludge age to synchronously reduce N2O production and carbon dioxide emissions owing to lower aeration energy without compromising the nitrification efficiency.