Due to the degradation reaction and the presence of acidic impurities (HCl, SO2, etc.) in the flue gas, heat stable salts (HSS) are widely present in the aqueous amine solvent for post-combustion CO2 capture. Accumulation of HSS in the solvent can lead to decreased absorption capacity and even corrosion of equipment in post-combustion capture (PCC) pilot plants. This study presents a novel “BMED+ED” two-stage electrodialysis unit for the efficient removal of HSS, including glycolate, formate, Cl−, and SO42−, from degraded amine solvent with an initial loading of approximately 0.38 mol/mol taken from the solvent loop of a PCC pilot plant after over 1000 hours of operation at real conditions. Experimental results showed that 94.93% of HSSs were removed with an initial HSS concentration of approximately 1920 ppm. The amine loss rate in the two-stage electrodialysis unit was much lower than that in a conventional ED unit, as protonated amine is further converted to organic amines by bipolar membrane electrodialysis. The energy consumption of the two-stage electrodialysis unit was 0.1643 kWh/L amine solvent, and the total cost for amine reclaiming was 1.8145 $/kg amine. This method effectively addressed the challenges of high amine loss rate in the traditional ED treatment process and hazardous wastewater disposal.