Abstract: The aim of this paper is to identify the effect of heavy metals (chromium, cadmium and lead) on wheat root’s growing up and their biological activities in soil with different fertilizer conditions were investigated. The effect of heavy metals (chromium, cadmium and lead) on wheat root’s weight was investigated by pot test, and their effects on amino nitrogen in soils were also studied after laboratory incubation under seven fertilizer systems with inorganic fertilizer, inorganic fertilizer with low straw manure, inorganic fertilizer with medium straw manure, inorganic fertilizer with high straw manure, inorganic fertilizer with low straw manure（fallow）, inorganic fertilizer with manure and control. The results showed that the effects of heavy metals (Cr、Cd and Pd) on wheat root’s weight were most obvious, Cr was the most harm to wheat root’s weight as well as their compound pollution was more serious more than single element. The study of laboratory incubation showed those effects of heavy metals on amino nitrogen in soil were most different with different fertilizer systems, especially the effect was very obvious under inorganic fertilizer system. On the contrary, those heavy metals’ inhibitions to total amino nitrogen in soil were lowest under inorganic fertilizer with low straw manure （fallow）. The study showed that people can control heavy metals’ activities in soils by adjusting fertilizer systems in practice. And people can decrease and control heavy metals’ pollution in soils by this way.