The harm of heavy metal on microorganism and the effect of bio-fertilizer on microorganism in polluted soil of apple root were studied. The results showed that the application of bio-fertilizer increased the amount of soil bacteria, jungi and actinomycete, especially for the bacteria. The amount of soil bacteria decreases sharp with the increase of Cd concentration from 10~30 mg/kg in soil. The effect of Cu is similar to Cd, but the degree of harm is less than Cd. Organic matter from bio-fertilizer can adsorb the dissociate cadmium and copper. The rate of adsorption increases with the increase of pH from 6 to 8. The rate of adsorption to copper is higher than cadmium under the condition of sourish soil. The bio-fertilizer can alleviate the damage of Cd and Cu to edaphons and that to Cu are more effective.