In order to improve the nitrogen removal efficiency and save operational cost, the feasibility of the alternating aerobic-anoxic process (AAA process) applied in a sequencing batch reactor (SBR) system for nitrogen removal was investigated. Under sufficient influent alkalinity, the AAA process did not have an advantage over one aerobicanoxic (OAA) cycle on treatment efficiency because microorganisms had an adaptive stage at the alternating aerobic-anoxic transition, which would prolong the total cycling time. On the contrary, the AAA process made the system control more complicated. Under deficient influent alkalinity, when compared to OAA, the AAA process improved treatment efficiency and effluent quality with NH-N in the effluent below the detection limit. In the nitrification, the average stoichiometric ratio between alkalinity consumption and ammonia oxidation is calculated to be 7.07 mg CaCO/mg NH-N. In the denitrification, the average stoichiometric ratio between alkalinity production and NO-N reduction is about 3.57 mg CaCO/mg NO-N. As a result, half of the alkalinity previously consumed during the aerobic nitrification was recovered during the subsequent anoxic denitrification period. That was why the higher treatment efficiency in the AAA process was achieved without the supplement of bicarbonate alkalinity. If the lack of alkalinity in the influent was less than 1/3 of that needed, there is no need for external alkalinity addition and treatment efficiency was the same as that under sufficient influent alkalinity. Even if the lack of alkalinity in the influent was more than 1/3 of that needed, the AAA process was an optimal strategy because it reduced the external alkalinity addition and saved on operational cost.