Zinc leaching residue is a hazardous solid waste with difficult treatment, high hazard and high yield, and it is a great challenge to treat it efficiently, harmlessly and economically among the various methods available. This paper introduced a micro-crystallization method to process zinc leaching residue into glass-ceramics with excellent performance and high value. The heavy metals in the raw material were well solidified in the glass-ceramics, eliminating the high hazard of heavy metals and other components. The bending strength, compressive strength, and Vickers hardness of the glass-ceramics prepared at the sintering temperature of 950 °C were 69.2 MPa, 434.3 MPa, and 6.66 GPa, respectively, while the water absorption, density, and acid and alkali corrosion resistance were excellent. The relationship between the microstructure and properties of glass-ceramics was investigated using traditional analytical techniques such as XRD, Raman, and SEM, and the mechanism of solidification of heavy metals Pb, Zn and Mn in glass ceramics were innovatively researched by the modified BCR sequential leaching test and XPS analysis. Anorthite and diopside ferrian were the two main crystalline phases in glass-ceramics. The sintering temperature affected the formation and growth of crystals, and determined the crystal size and crystallization rate, thus affecting the properties of glass-ceramics. Part of the heavy metal was solidified in the amorphous phase in the glass-ceramic, and the other major part entered the crystal as an impurity substitution to form a solid solution at a specific location. The zinc leaching residue based glass-ceramic had been studied, which was pioneering and with excellent performance and environmental safety. Thus, the safe and economical treatment of these hazardous wastes promotes the clean, green and efficient development of related industries.