As a form of solid waste, electrolytic manganese residue (EMR) exhibits low reactivity, high sulfate content, and exceeds the standards for heavy metals. To address these drawbacks, a high-temperature thermal activation method was employed to enhance its reactivity and remove pollutants. The study investigated the physicochemical properties and leaching toxicity of EMR under different thermal activation conditions. Additionally, the thermally activated EMR was utilized in the preparation of geopolymer material, and the influence of EMR activation temperature, EMR content, sodium silicate content, and molar ratio on the mechanical properties, hydration mechanism, microstructure, and leaching toxicity of the EMR geopolymers was analyzed. The results indicated that after activation in the temperature range of 0–1200°C, the active content of silica-alumina in EMR increased, sulfate decomposition occurred, and the leaching of Mn2+ and NH4+-N decreased to 21.24 and 0.576 mg/L, respectively. When the activation temperature reached 1200°C, the compressive strength of the geopolymer, prepared with 50 % EMR, 50 % granulated blast furnace slag (GBFS), 30 % sodium silicate, and a molar ratio of 1.2, could reach 53.2 MPa at 28-day. Under activation in the range of 0–800°C, ettringite was abundant in the geopolymers, providing strength support. With activation in the range of 800–1200°C, the geopolymers became denser, exhibiting flaky and agglomerate gels. A diffraction peak appeared at 20°-40°(2θ) corresponding to C-(A)-S-H and N-S-A-H gels. Due to the slow depolymerization-polymerization kinetics of the EMR geopolymer and high sulfate content, the heat release rate and cumulative heat were significantly lower than ordinary portland cement (OPC). In the structure of EMR geopolymer, Mn2+ replaced Na+ and Ca2+ in the silicoaluminate structure or chemically bonded with anionic groups to the geopolymer. Simultaneously, Mn2+ participated in the formation of the EMR geopolymer gel, encapsulating within the gel. Therefore, the leaching of pollutants from EMR geopolymers met the standards of GB8978–1996.