This chapter presents a new method for treatment of heavy metal ions in soil or water. Heavy metal pollution in soil and water has become one of the serious environmental problems. Heavy metal pollution can degrade soil quality and ecosystems, contaminate crops, and threaten human health. At present, there are three ways to repair heavy metals in soil or water, including physical, chemical, and biological technologies. The microbial mineralization technology can be applied to remove heavy metal pollutants which contaminated soil and water and has been paid with more attention in recent years. Heavy metal ions can be mineralized by phosphate-mineralization microbe to form stable phosphate nanomaterials compared to mineralization of carbonate-mineralization microbe in the environments. Therefore, heavy metal pollution can well be removed from soil or water by microbial mineralization method.