Abstract: To investigate the effects of long-term fertilization on accumulation and availability of Cd, Zn and Cu in a paddy soil, a field experiment was conducted since 1986. There were five treatments, including the control (no fertilizer, CK), chemical fertilizers (NPK), straw returning (ST), lower organic fertilizer (LM) and high organic fertilizer (HM) with similar N application rate. The total and available concentrations of cadmium (Cd), zinc (Zn) and copper (Cu) in the paddy soil and total concentrations of Cd, Zn and Cu in rice tissues were determined. Further, the relationships among the total and available concentrations of heavy metals in soil, the soil basic properties and the concentrations of heavy metals in brown rice were analyzed. The results indicated that the treatments of NPK and ST treatments have limited effect on accumulation of Cd, Zn and Cu in the soil. However, long-term application of organic fertilizers significantly increased soil total and available Cd, Zn and Cu by 35.00%~80.00%, 63.91%~82.55%, 118.41%~180.21% and by 28.57%~71.43%, 407.12%~783.15%, 336.59%~573.17%, respectively, as compared with the CK treatment. Compared to the CK treatment, the concentrations of Cd and Cu in brown rice of LM and HM significantly increased by 100.00%~150.00% and 63.30%~85.64%, respectively. Further, the correlations between soil total and available Cd, Zn, Cu and soil properties might indicated that the accumulation of heavy metals in soil was related to the high concentrations of Cd, Zn and Cu in organic fertilizer and the increase of soil total P could affect the availability of heavy metals in soil. In conclusion, long-term application of organic fertilizer can effectively improve the soil fertility, but could result in accumulation of Cd, Zn and Cu in the soil and subsequently in rice grain. Although, the concentrations of Cd and Cu in brown rice were lower than the limit standards of China, the risk enhancement of heavy metals in paddy soils should be paid more attention. When organic fertilizers were used to improve soil fertility, the concentrations of heavy metals in such fertilizers should be subject to careful control.