The flue gas desulfurization wastewater is highly saline and has too many refractory pollutants to be recycled during the desulfurization process of the coal-fired heating plant. Given that waste heat is abundant in coal-fired heating plants, a thermal treatment method was developed to simultaneously remove sulfates and nitrates from the wastewater, with the production of chemical-grade natroalunite and recycled water. The results showed that sulfates and nitrates were 50.3 and 10 g/L in the wastewater, respectively, and only 2.8% and 9.1% were removed after direct treatment at 270°C for 7 h; but these rates increased to 99.3% and 99.9%, respectively, with the addition of commercial poly aluminum chloride. Mass balance summarized that the treatment of 1 ton wastewater needed 0.1 ton PAC and produced 0.11 ton natroalunite and 0.92 ton recycle water. The removal of sulfates and nitrates was mainly done by the precipitation reaction of sulfates such as natroalunite and the redox reaction between nitrates and organics, respectively. Thermodynamic analysis demonstrated that the precipitate reaction occurred at 45°C and accelerated in the temperature range of 45–270°C, but became slow with the decrease of sulfate and Al concentrations in wastewater. Four other reagents were also used for wastewater treatment in comparison with PAC and showed the following order of performance: PAC > citrate calcium > limestone > subacetate aluminum > citrate ferric. This method provided a practical route to treat wastewater from flue gas desulfurization without generating secondary waste.