Partial nitrification (PN) was rapidly started-up in a sequencing batch membrane bioreactor (MBR) treating domestic wastewater with low temperature (11~15°C), the influence of alkalinity on PN process and the feasibility to control the ratio of nitrite to ammonia in effluent were investigated through changing the ratio of Alkalinity/ammonia in influent. Results showed that effluent ratio can be controlled flexibly with the liner relationship between ammonia conversion and the ratio of alkalinity to ammonia when alkalinity is insufficient, whereas, that could be effectively achieved by the indicator role of alkalinity on nitrite. Phylogenetic results indicated the predominance ofNitrosomonasand the absence of theNitrosospirain the condition of insufficient alkalinity, which was consistent with the SEM results. FISH results suggested that lack of alkalinity presented little impact on the relative quantity of AOB.