Fertilization of crops with pig manure is a common practice throughout the world. Nevertheless, due to the relatively high copper (Cu) and zinc (Zn) contents in pig manure, continuous application of pig manure could have negative effects on soil and plant. The study aimed at the impacts of long-term applying different pig manure rates (equivalently 0, 100, 250 and 500 kg total N/ha/year from 2002 to 2008 and 0, 10, 25 and 50 t fresh weight/ha/year from 2009 to 2011, respectively) on Cu and Zn accumulation in soil and plant. During the 10 years of the experiment, a total of 2.04 to 10.20 kg/ha/year for Cu, 3.15 to 15.73 kg/ha/year for Zn were applied to the soil. Results from this study showed that long-term pig manure application resulted in serious accumulation of Cu and Zn in soil, total Cu and Zn concentrations increased by 204% and 107% at high application rates, respectively. Although topsoil Cu and Zn concentrations were below concentrations considered phytotoxic to crops, according to current Chinese legislation, it would take only less time than 16 and 27 years of high application rates to reach the allowable limits. Our result also suggested that Cu and Zn leaching occurred in the tested soil. The Cu and Zn concentrations in stalks and grains were not affected by the application of pig manure, and these values were lower than the threshold values for animal and human ingestion.