Dealing with nitrogen-rich saline wastewater produced by industries remains challenging because of the inhibition of functional microorganisms by high salinity. The underlying mechanisms of anaerobic ammonium-oxidizing bacteria (AnAOB) exposed to salinity stress should be studied to investigate the potential of anaerobic ammonium oxidation (ANAMMOX) for applications in such wastewater. In this study, the total DNA from granular sludge was extracted from an expanded granular sludge bed (EGSB) reactor operated at 0, 15 and 30 g/L salinity and subjected to high-throughput sequencing. The nitrogen removal performance in the reactor could be maintained from 86.2 to 88.0% at less than 30 g/L salinity level. The microbial diversity in the reactor under saline conditions was lower than that under the salt-free condition. Three genera of AnAOB were detected in the reactor, and Candidatus Kuenenia was the most abundant. The predictive functional profiling based on the Clusters of Orthologous Groups of proteins (COGs) database showed that the inhibition of AnAOB under saline conditions was mainly characterised by the weakening of energy metabolism and intracellular repair. AnAOB might adapt to salinity stress by increasing their rigidity and intracellular osmotic pressure. The predictive functional profiling based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database revealed that the inhibition of AnAOB was mainly manifested by the weakening of intracellular carbohydrate and lipid metabolism, the blockage of intracellular energy supply and the reduction of membrane transport capacity. AnAOB might adapt to salinity stress by strengthening wall/membrane synthesis, essential cofactors (porphyrins) and energy productivity, enhancing intracellular material transformation and gene repair and changing its structure and group behaviour. The stability of the nitrogen removal performance could be maintained via the adaptation of AnAOB to salinity and their increased abundance.