An internal-circulate sequencing batch airlift reactor (IC-SBAR) has been developed to evaluate the efficiency of phenol and ammonia removal in treating synthetic wastewater. This study examined the effect of operation cycle on this system. Results showed that above 97.0% removal efficiencies of ammonia and phenol were achieved, which indicated that ammonia and phenol removals were not related to operation cycle. The average removal efficiency of 91.7% for chemical oxygen demand (COD) was achieved when the static/aerobic/settling time was 240 min/440 min/40 min. It was found that COD removal efficiency increased due to the time of operation cycle being prolonged. The average removal efficiencies of total inorganic nitrogen (TIN) were 65.8, 69.3 and 68.9% when average TIN concentrations were 78.0, 97.6 and 88.4 mg/L, respectively, in the influent. A cycle study showed that most phenol was degraded by aerobic microbes. Increasing the static time from 120 to 240 min resulted in the accumulation of NO2−-N, which indicated that the structures of the nitrifying bacterial community were changed.