The invention discloses a method for preparing a microbe-modified clay mineral material. The method comprises the following steps: inoculating microbe bacterium powder in a microbe medium containing clay minerals, culturing for 7 days by a constant temperature shaking table, calcining the material and adding hydrogen peroxide, performing secondary calcining in a muffle furnace at the temperature of 200 DEG C until no moisture is generated, grinding the raw material, passing the material through a 120-mesh sieve to obtain the microbe-modified clay mineral material. The microbe-modified clay mineral material has the advantages that 1) the material can obviously increase the adsorption capability of the original clay mineral to the heavy metal cation; 2) the material is the environmental protection material and is used for recovering the heavy metal-polluted water body and soil without secondary pollution; and 3) after the clay mineral is modified by the microbe, an inner structure of the clay mineral is changed, the heavy metal is fixed on an interlayer of the clay minerals, and the long-term effectiveness of the passivation effect can be guaranteed. The material can be used for recovering the heavy metal-polluted water body and soil.