Display omitted •Aerobic granules SNDPR used for hypersaline wastewater treatment.•Reliable nitrogen removal efficiency was achieved at elevated salinity.•EBPR was deteriorated with 2 % (w/v) salinity stress.•Salinity induced changes in granular community structure.•Halophilic and non-halophilic bacteria were recognized. Hypersaline wastewater may pose threats to biological wastewater treatment processes. An aerobic granular sludge-based sequencing batch reactor (SBR) performing simultaneous nitrification, denitrification and phosphorus removal (SNDPR) was evaluated with increased salinity from 1 to 2 % (w/v). Nitrogen removal performance was unaffected by salinity up to 20 g/L in terms of reliable and efficient nitrification and denitrification. Enhanced biological phosphorus removal (EBPR) process was completely deteriorated at salinity up to 2 %, in contrast to excellent phosphorus removal at 1 %. Profiles of phosphorus over one cycle demonstrated that higher salinity not only inhibited anaerobic phosphorus release but also impeded aerobic/anoxic phosphorus uptake. Illumina MiSeq sequencing revealed multiple halophilic and non-halophilic bacteria within aerobic granules with family Anaerolineaceae being the predominant potential salt adapter. Besides, ammonia oxidizing bacteria (AOB), glycogen accumulating organisms (GAOs) were more tolerant to salt than nitrite oxidizing bacteria (NOB) and phosphorus accumulating organisms (PAOs) and denitrifying PAOs (DNPAOs). These results deciphered the resilience of aerobic granular sludge-based biological nitrogen and phosphorus removal processes to hypersaline stress.