Halophilic aerobic granular sludge (HAGS) can effectively treat saline wastewater characterized as high salinity and change of salinity, which was discharged from various industries. The stable microbial community ecology is the key to successful operation of HAGS, while its change and outcome under varying salinities is unexplored. In this study, HAGS systems under different salinities were studied to elucidate microbial community ecology process and its effects on HAGS. The study found that the salinity variation intensified competition interaction of bacteria and fungi due to the niche overlap. The decreased salinity from 40 to 0 g/L resulted in functional bacteria loss and fungal population increase by 94.46 %. The HAGS disintegration was caused by insufficient extracellular polymeric substances, which were secreted by bacteria and fed by fungi. This study is the first to reveal role of microbial community ecology on stability and function of HAGS in response to salinity variation.