In order to study the effects of conventional and organic cropping systems on soil quality, experiment was conducted by choosing topical organic farms, for studying soil physical and chemical properties and the concentrations of soil heavy metals including Cu, Zn, Pb, Cd, Cr, As, Hg under different cropping systems. Results showed that compared with the conventional cultivation, organic farming reduced soil bulk density and improved the MWD and GMD of soil water stable aggregate, reduced soil aggregate fractal dimension D, showing that organic farming effectively improved soil pore structure and the quantity and stability of water stable soil aggregate. The content of soil organic matter in organic farming increased by 20% – 80% and the concentration of nitrogen, phosphorus, potassium in soil were also increased significantly, indicating that organic farming is beneficial to improve soil fertility. Compared with the background value in the investigation area, the content of Cu, Zn, Pb, Cr, Cd, Hg, As in soil increased and accumulated in different degree. Compared with conventional farming, organic farming on the whole effectively reduced the threat of Cr, Cd pollution in soil. There was obvious enrichment and accumulation of Cu, Zn, As in organic wheat farms because of different quality of organic manure. Compared to conventional farming, organic farming was conductive to improve soil structure, increase soil fertility, reduce the overall risk of soil heavy metal pollution, the development of organic agriculture can improve soil quality comprehensively. The risk of heavy metal pollution in soil mainly because the quality of organic fertilizer, organic farming should strengthen monitoring of organic fertilizer.