Simultaneous partial nitrification, ANAMMOX and denitrification (SNAD) process was applied to remove ammonium and COD from wastewater in an intermittent aeration membrane bioreactor (MBR). The operating parameters (influent carbon to nitrogen ratio (C/N), alternating aerobic/anaerobic (T-ae/T-an) period and air flow) were optimized through response surface methodology (RSM). The optimal operating parameters were: a C/N of 0.42-0.55, a T-ae/T-an of 1 min/(2.5-3.1) min and an air flow of 0.48-0.51 L min(-1). Under these conditions, the mean N2O and NO (biogas) emissions were 2.0% and 0.17% of the total incoming nitrogen, respectively. For the SNAD process, stoichiometric modeling results indicated that total nitrogen (TN) removal by ANAMMOX was 76.1%, and that heterotrophic denitrification was responsible for 19.0% of TN removal and 95.0% of COD removal. Photo of SNAD granules, scanning electron microscopy (SEM) and fluorescence in situ hybridizations (FISH) analysis proved the co-existence of AOB, ANAMMOX and denitrifying bacteria in the reactor, and showed that the biomass in the outer part of the SNAD granule was mostly AOB, while ANAMMOX and denitrifiers were in the inner anoxic part. These results provide useful information for the application of the SNAD process. (C) 2016 Published by Elsevier Ltd.