Based on a long-term experiment in Shenyang Experimental Station, the effect of manure application on the contents and budgets of Cu, Zn and Cd in the arable soil was studied. The experiment included four treatments: no mature addition (CK), mature addition 10 t·ha-1 year-1 (M1), 25 t·ha-1 year-1 (M2), and 50 t·ha-1 year-1 (M3). The result showed that Cu, Zn and Cd in soil were accumulated with manure application and prolongation of experiment, and the accumulative magnitude increased with increasing of manure application. The average annual growth rates of the heavy metals in the four treatments (CK, M1, M2, M3) were 2.83%, 6.56%, 7.54%, 8.96%; 0.03%, 3.44%, 4.53%, 6.64% and 1.51%, 8.01%, 10.27%, 16.08% for Cu, Zn and Cd, respectively. After six years of the experiment, the content of Cd in the M3 treatment was quite close to the threshold of Chinese Soil Quality Standard Grade III (1 mg·kg-1, GB15618—1995). After 12 years of the experiment, the contents of Cu in the mature-amended treatments fell in the Chinese Soil Quality Standard Grade III, which should be paid more attention. Although the heavy metals in soil were gradually accumulated, the Cu, Zn and Cd levels in crop grain were still below the National Food Contamination Standards (GB2762—2005; GB13106—91; GB15199—94), indicating the contents of heavy metals in crop produced from contaminated soil might not exceed the corresponding standards. The contents of Cu, Zn and Cd in the straw were much greater than those in the grain. The removal of heavy metal by crop was in the order of M3>M2>M1> CK. The average amounts of Cu, Zn and Cd annually removed from the soil in the four treatments (CK, M1, M2 and M3) were 35.68, 47.80, 63.65, 69.64; 249.14, 375.22, 375.16, 444.44, and 0.83, 1.39, 1.64, 1.66 g·ha-1, respectively. The contents of heavy metals in organic manure varied in different years: the contents of Cu and Zn increased year by year, while Cd presented a decreasing trend. The average amounts of Cu, Zn and Cd annually remained in the soil in the treatments M1, M2 and M3 were 2 283.0, 5 763.7, 11 585.4; 2 483.3, 6 771.4, 13 849.2 and 4.8, 13.9, 29.5 g·ha-1, respectively. Since the heavy metals in organic manure markedly fluctuated in different years, the average residuals can only reflect the changing trend. Therefore, the residuals of heavy metals in the soil could be accurately predicted only according to status of manure in a given year.