The environmental quality of heavy metals (Pb, Cd, Cr, As, Hg) in agricultural surface soil of Chongming Island was assessed by national, local and professional standards based on a large scale investigation, in which 28 samples from vegetable plots, 65 samples from paddy fields and 9 samples from watermelon fields were collected from whole island area. Results showed that the average concentration of Pb, Cd, Cr, As and Hg was 21.6 mg·kg-1 , 0.176 mg·kg-1, 69.4 mg·kg-1, 9.209 mg·kg-1 and 0.128 mg·kg-1, respectively. Compared with the background value of Shanghai City soil, except for Pb and Cr, all the other heavy metals average concentrations in Chongming Island agricultural surface soil exceeded their corresponding natural-background values. The concentrations of Cd, As and Hg were 33.0%, 1.2% and 26.3% higher than the background value of Shanghai City, respectively. In addition, inverse distance interpolation (IDW) tool of GIS was also applied to study the spatial variation of heavy metals. The results indicated that most of agricultural soil quality was good, and the ratio of ecological, good soil, certified soil and disqualified soil were 1.26%, 97.1%, 1.47% and 0.12%, respectively. About 10.1%, 85.7%, 27.0%, 55.4% and 55.2% soil samples exceeded the Pb, Cd, Cr, As and Hg background value of Shanghai City, respectively. Among these three land use type soils, vegetable soil was most seriously polluted by heavy metals, which is probably related to the over-application of pesticides. The annual deposition fluxes of Pb, Cd, As and Hg were 7736 μg·m-2·a-1, 208 μg·m-2·a-1, 2238 μg·m-2·a-1 and 52.8 μg·m-2·a-1, respectively. Crop straw burning was the important source of heavy metals of atmospheric deposition, and atmospheric deposition contributed a lot to heavy metals in agricultural soil in Chongming Island.