This paper proposes a green environment-friendly Bacillus subtilis to mineralize and consolidate waste incineration fly ash and heavy metal cations, and there is no harmful by-product in the mineralization process. Different phosphate products can be prepared, and are more stable than the microbially-induced carbonate precipitation (MICP) in nature. Typical heavy metal oxides were mainly PbO, ZnO, CdO, NiO, CuO and CrO in the chemical composition of waste incineration fly ash. Microstructure and chemical composition of waste incineration fly ash before and after treatment were characterized by powder X-ray diffraction (XRD) analysis and scanning electron microscopy. Scanning electron microscopy (SEM) images showed that the morphology of the Bacillus subtilis was mainly a rod-like structure. The optimal hydrolysis dosage of the organic phosphate monoester sodium salt was 0.2mol in the bacterial solution (1L, 20 g/L). The optimum required mass of the bacterial powder was 15 g/kg in treatment process of the waste incineration fly ash. The initial concentration of lead ions was 40.28 mg/L in waste incineration fly ash solution. After the optimum dosage treatment, the removal efficiency of lead ions was 78.15%, 79.64%, 77.70% and 80.14% when curing time was 1, 2, 4 and 6d, respectively. The waste incineration fly ash had a Shore hardness of 22 after the optimum amount of bacterial liquid treatment. Results of wind erosion test showed that the wind erosion rate of waste incineration fly ash was 2.6, 0, 0, 0, 0 and 0 g/h when blank group, deionized water, 100, 200, 300 and 400 mL of bacterial solutions treated, respectively. The bio-mineralization method provides an approach for the safe disposal of heavy metals in the contaminated areas of tailings, electroplating sewage, waste incineration plants, and so on.