Many minerals in nature have the self-purification capacity to hold and stabilize deleterious contaminants into their lattice structures, which can be used for treatment of heavy metals-bearing contaminants. Hydrotalcite Layer Double Hydroxide (LDH), tobemorite Calcium Silicate Hydrate (CSH) and apatite are ubiquitous minerals in nature, having higher geochemical stability and potential for binding and stabilizing heavy metals. Based on the elucidation of crystal structure property and self-purification principles of the three minerals above, this article discussed how to design the self-purification system of heavy metal-bearing contaminants.