Aiming at improving phytoremediation of Cd-, Pb- and Zn-contaminated soil, a pot experiment was carried out using Brassica juncea as a hyperaccumulator to explore effects of Bacillusme gaterium and Bacillus mucilaginosus compound (Treatment A) and Aspergillus niger ferment (Treatment B) on phytoremediation of Cd-, Pb- and Zn-contaminated soil. Results show that Treatment A not only promoted growth of the hyperaccumulator by 24.73%, but also helped improve availability of Cd, Pb and Zn in the soil by 15.02%, 7.65% and 2.23%, respectively, thus increasing Cd, Pb and Zn uptake by 52%, 121% and 23%, respectively, and eventually improving significantly the effect of phytoremediation. In light of their effects on physiological and bio-chemical indexes (SOD, POD and CAT), Treatment A was less harmful than Treatment B to the hyperaccumulator. So the microbial compound in Treatment A is an effective one that has a high value in use in the field of phytoremediation of contaminated soils. However, Aspergillus niger ferment is not suitable for the phytoremediation of contaminated soils.