Resource utilization of livestock manure has been encouraged vigorously in China. To explore the potential risks of heavy metal accumulation in paddy fields under “swine-rice” nutrient management option, a 5-year field-scale experiment was conducted in this study. A swine farm with manure fully treated and returning to field was selected as the case-study farm to monitor and track the migration regularity of six heavy metals in the paddy soil. The results showed that the heavy metals such as As, Cr, Pb, Cu, Zn and Cd were detected in the feed, and the content of Cu and Zn was much higher than the recommended addition amount in NY/T 65-2004 “Standard for Pig Feeding”. The content of heavy metals in the manure showed the characteristics of “high in autumn and winter and low in spring and summer”. Among them, the contents of Cr, Cu, Zn and As in the manure in winter were the highest, which were 115.9, 1 150.1, 1 630.0, and 2.62 mg·kg-1, respectively. The contents of As, Cr, Cd, Cu and Zn in the plough layer (0-20 cm) soil of the supporting farmland showed an obvious accumulation trend, while Cu and Zn was accumulated obviously, and the average accumulation rate was as high as 5.13 and 2.29 mg·kg-1, respectively. Heavy metals all migrated to the deep soil, and Pb, Cu, Zn, Cd generally showed a certain vertical decreasing change, while the content of As and Cr in the deep soil increased, showing a leaching down characteristic. Through the analysis of fate characteristics, it was found that the content of Cd in rice accounted for 9.11% of the total input, which was much higher than the other types of heavy metals. Therefore, it is necessary to strictly control the amount of feed additives containing Cu, Zn, and Cd in livestock production and standardize the swine manure disposal and utilization management, to reduce the risk of heavy metal pollution in farmland soils.