Based on an 11-year fertilizer field trial (located at the lower liaohe river plain), the effects of different organic manure application rates on the accumulations of heavy metals (Cu, Zn, Cd and Cr) in surface soil (0～20 cm), and the leaching characteristic and vertical migration pattern of heavy metal have been investigated in this rainfed agro-ecosystem using undisturbed soil columns. The result showed that the content of heavy metal in surface soil was elevated with the increase of manure application. The increasing magnitude was in the order of Cd>Cu>Zn>Cr. According to the Chinese soil quality standard (GB15618—1995), the application of manure (not exceeding 50 t·ha-1) did not result in serious heavy metal pollution in the surface soil. Chromium met the Grade Ⅰ, and Cu and Zn met the Grade Ⅱ; whereas, Cd was almost exceeded the threshold of Grade Ⅲ. The potential risk of Cd in soil should be paid more attentions in future research. According to the National water quality standard (GB/T14848—93), the Cu and Cd concentrations in leachate samples were up to the Grade Ⅱ except only a few samples that fell in Grade Ⅲ. Furthermore, Cr in the leachate all matched Grade Ⅰ water quality standard. These results indicated long-term application of manure (not exceeding 50 t·ha-1) in our site had not induced contaminant risks of heavy metals in underground water. In addition, the Cu, Zn and Cd (except Cr) in leachate all declined with the increase of soil depth, indicating the low capacity of vertical migration of heavy metal. Among the four heavy metals, Zn and Cr tended to be leached into deep soil, whereas Cu and Cd were more prone to be accumulated in surface soil.