Soil pollution by heavy metal has been gradually serious in facility agriculture. Due to the interaction of soil minerals, organic matter and microorganisms at natural condition, the combination mechanism between soil single component and heavy metal couldn't represent the reality of the translocation and transformation of heavy metal in the soil. In this research, mechanical mixture of montmorillonite and kaolinite (Mont:Kao=1:1), Gram-positive(Bacillus subtilis, B.s) and Gram-negative (Pseudomonas putida, P.p), and humic acid (HA) were selected as phyllosilicates mineral in vegetable greenhouse and farmland soil, organic matter and bacteria respectively. Cd²⁺ and Cu²⁺ were taken as the target compounds. The adsorption mechanism and interaction on the binding of Cd²⁺ and Cu²⁺ by the ternary composites of Mont/Kao-HA-bacteria were investigated by macroscopy sorption together with XRD, ATR-FTIR and SEM. The experimental results showed that heavy metal ions had the additivity of sorption on Mont/Kao-HA or Mont/Kao-bacteria system, while the antagonism between heavy metal ions and the ternary Mont/Kao-HA-bacteria system. The kinetics data of Cu²⁺ adsorption on mesoporous goethite fitted well the pseudo-second-order equation. The maximum Cu²⁺ adsorption capacities followed the order:B.s > P.p > Mont/Kao-B.s > Mont/Kao-P.p > Mont/Kao-HA-P.p > Mont/Kao-HA > Mont/Kao.