In the process of flue gas desulfurization and denitrification, the generation of high-sulfate wastewater containing nitrogen is a significant challenge for biological wastewater treatment. In this study, halophilic activated sludge was inoculated in a Sequencing Batch Reactor to remove nitrogen from wastewater with a high sulfate concentration (60 g/L). With the influent concentration of 180 mg/L, the removal rate of total nitrogen was more than 96.7%. The effluent ammonium nitrogen concentration was lower than 1.94 mg/L, and the effluent nitrate nitrogen and nitrite nitrogen concentrations were even lower than 0.77 mg/L. The salt tolerance of activated sludge is mainly related to the increase in the content of ectoine in microbial cells. The Specific Nitrite Oxidation Rate is quite low, while the Specific Nitrite Reduction Rate and Specific Nitrate Reduction Rate are relatively strong. In the system, there are various nitrogen metabolic processes, including aerobic nitrification, anaerobic denitrification, and simultaneous nitrification-denitrification processes. By analyzing the nitrogen metabolic mechanisms and microbial community structure of the reaction system, dominate bacteria can be identified, such as Azoarcus, Thauera, and Halomonas, which have significant nitrogen removal capabilities.