A long-term fertilization experiment, designed to have nine treatments varying in application rates of N, P, K and pig manure, with or without incorporation of rice straw to the field, was carried out to determine effect of these treatments on the concentrations of Cu, Zn, Fe, Mn, Pb and Cd in soil, rice plant and brown rice. Results showed that the total soil Cu, Zn and Cd concentrations in Treatment MS(application of pig manure with incorporation of rice straw to the field), NMS(application of N, pig manure with incorporation of rice straw to the field) and NPKMS(application of N, P, K, pig manure with incorporation of rice straw to the field) were significantly higher than in the other treatments, however, they were not significantly different from each other in total soil Fe, Mn and Pb. Compared with CK(no fertilizer), all the fertilization treatments increased soil available Cu, Zn and Fe, and, the MS, NMS and NPKMS treatments did soil available Cu, Zn and Cd, significantly, but did not differ much in soil available Pb between the treatments. The Cu, Zn, Fe, Mn and Pb concentrations in brown rice varied slightly or insignificantly from treatment to treatment. However, the Cd concentration in brown rice in Treatments MS, NMS and NPKMS was higher than the upper limit of the criteria (>0.2 mg kg^-1) of the National Standard for Food Hygiene for Cd concentration. The amounts of Cu, Zn, Fe, Mn, Pb and Cd absorbed by rice plant and accumulated in the aerial part the plant was positively related with the biomass of the aerial part. Soil available Cu, Zn and Cd concentration was positively correlated with the total soil Cu, Zn and Cd concentrations in the soil, and only the concentration of Cd in brown rice could be predicted through total and available concentrations of Cd in the soil. Attention should be paid to the soil Cd pollution caused by long-term application of pig manure containing high concentrations of heavy metals.