Heterotrophic nitrification-aerobic denitrification (HN-AD) is a novel alternative for nitrogen removal due to simultaneous nitrification and denitrification that occurs under aerobic conditions. Until now, ways in which to achieve aerobic nitrogen removal from wastewater via the HN-AD process have not been fully explored. In this study, autotrophic nitrification was converted into HN-AD in a halophilic aerobic granular sludge (HAGS) system when the wastewater salinity decreased from 30 to 20 g/L. Bacteria affiliated to the genus Paracoccus were dominant in the HAGS with a relative abundance of 56%, functioning with HN-AD. Accordingly, the indicative gene napA encoding for HN-AD was 5.1 × 109 copies/g HAGS. HAGS performing HN-AD exhibited a stable total inorganic nitrogen (TIN) removal efficiency performance in response to salinity variations of 10–40 g/L, owing to the stable HN-AD functional community. The significant inhibition of HN-AD was observed in both low salinity (≤5 g/L) and high salinity (≥50 g/L) conditions, accompanied by the disintegration of granules. Granular disintegration was triggered by the lower secretion of extracellular polymeric substances and alginate-like exopolysaccharides. HAGS performing HN-AD could simultaneously remove chemical oxygen demand and TIN from saline wastewater in a single aerobic tank, thus reducing the construction and operation costs.