Electrolytic manganese residue (EMR) stored in the residue yard contains a large amount of manganese (Mn2+) and ammonia nitrogen (NH-N), which can easily migrate and pollute the surrounding environment. Therefore, the physical and chemical properties of EMR with different storage time (3 months to 10 years), such as pH, water content, conductivity, total metal content, leaching toxicity, chemical morphology and phase structure, were systematically studied. The phase composition, micro morphology and surface electronic valence of EMR with different storage time were analyzed by XRD, SEM and XPS. The results showed that with the storage time increased, pH, the water content, electrical conductivity and the contents of soluble Mn2+, Ca2+, Mg2+, Se4+ and NH-N decreased. Exchangeable and carbonates bound Mn were the main forms of Mn loss. EMR stored for 10 years still had a great risk of environmental pollution. The total amount of Cu, Cr, Cd, Pb, and Zn far exceeded the background value of Guangxi soil. The leaching concentration of Se4+ was 11 times of the concentration limit in 《Identification standards for hazardous wastes—Identification for extraction toxicity》 (GB 5085.3—2007). The leaching concentration of Mn2+ and NH-N were 102 times and 45 times of the first class standard limit of 《Integrated wastewater discharge standard》 (GB/T 8978—1996). The main forms of Mn2+ and NH-N in EMR with different storage time were (NH4)(Mn,Ca,Mg)PO4·H2O, (NH4)2SO4, MnSO4·H2O, MnCO3, Mn2O3 and MnO2. Iron-containing phases mainly included FeS2, FeOOH, Fe3O4 and Fe2O3. And it also contained clay minerals, including Al4(OH)8(Si4O10), Al2Mg4(OH)12(CO3)·3H2O and KAl(SO4)2·12H2O. In addition, with increasing storage time, the average pore size of EMR decreased, and the phenomenon of crisscross inclusion of massive, columnar and ball like particles increased. The Fe(OH)3 colloid particles gradually transformed into FeOOH, Fe2O3 and other iron-containing phases. The research results provided basic theoretical support for the harmless treatment and resource utilization of EMR.