New-energy industry produce large amount of emerging high-speed battery jarosite slag, containing Mn and Ni, which is large in quantity and harmful. Harmless treatment is in urgent need. We research on the curing mechanism of heavy metals migration and transformation during phase via iron clusters transformation in glass-ceramics. Based on first-principles and density functional theory, regulating electronic structure of Mn2+ and Ni2+ by Cr3+. After clarifying the interaction among curing compatibility, capacity and stability, the structure-activity relationship among electronic & molecular structure and leaching concentration of heavy metals was established. The results show that CaNiSi2O6 is difficult to cure Ni2+, the formation of iron clusters promotes the conversion of multiphase to Fe-Spinel A; Mn2+, Ni2+ went into the octahedron in Fe-Spinel A cannot be stabilized; Cr3+ promotes migration of Mn2+, Ni2+ into the tetrahedral, turning Fe-Spinel A into Fe-Spinel B, improves curing compatibility of Mn2+, Ni2+; Cr3+ also adjust the bond structure, which enhances solid solution attraction to Mn2+ and Ni2+, and capacity of Mn2+ and Ni2+ increases from 19%, 30%–147%, 195%; improving compatibility and capacity of Fe-Spinel reduces leaching concentration of Mn2+ and Ni2+ from 1.32, 0.51 mg/L to 0.48, 0.03 mg/L. This work realizes the harmless disposal of recycling Mn- and Ni-rich battery slag. The solidified body can also be reused as eco-friendly resource.