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Heavy metal contamination of soil may pose risks to human health and ecosystem environment. Phytoremediation is a low-cost and ecologically sustainable way to remediate heavy metal contaminated soils. As most of the heavy metal accumulator plants are low biomass producers, we selected maize as our experimental phytoremediation plant, which can both produce large useful biomass and remediate heavy metal contaminated soils. The effect of humic acid and bacterial manure on heavy metal accumulation in different organs of maize was studied in this paper, in order to investigate whether the fertilizer application has an effect on phytoremediation efficiency. The results showed that Cu, Pb and Zn contents in the organs of maize generally followed the order root>stem≈leaf>grain. Application of humic acid and bacterial manure improved the contents of Cu, Zn and Pb in different organs compared with those without fertilizer application. Maize with humic acid application generally had higher contents of Cu, Zn and Pb in the organs than that with bacterial manure application. This study indicated that fertilizer application was possibly one of the efficient ways to enhance the efficiency of soil phytoremediation.