There is growing concern about heavy metal pollution in peri-urban areas with the rapid development of urbanization in China. In this paper, the balances of some heavy metals including Cu, Pb, Zn and Cd at small-scale vegetable farming system were studied during the years between July 2003 and July 2005 in an industry-based peri-urban area, Wuxi of the Yangtze River Delta region of China in order to judge the trend of heavy metal accumulation in the agricultural eco-system and assess the healthy risk of heavy metals in soils and vegetables. Results showed that organic fertilizers contributed mainly to heavy metal input in the studied system, which accounted for more than 88.5% of the total input of heavy metals. The inputs of heavy metal in the studied area were higher if compared to yearly heavy metal inputs in European agricultural area, while the corresponding outputs of heavy metals were obviously low, only accounting for less than 10% of the total inputs. Consequently, Cu, Pb and Zn balances were positive in all plots. Heavy metal contents in the studied plots were all lower than the limits according to Chinese agricultural soil safety standard level 2, but higher than the background value of Anthrosols in Tai-hu Lake region. Assessment of healthy risk indicated a high risk of heavy metal pollution existed in the leaf vegetables in the studied area.