This experiment was conducted since 1989 to study soil Hg balance and transfer with soil depth under the influence of long-term fertilization. Hg contents of surface soils in different treatments increased first and then decreased, in an order of NPK≈NP≈PK≈OM+NPK (Half organic fertilizer + Half chemical fertilizer) > OM (Organic fertilizer) >NK≈CK (Control, no fertilization). Hg contents in some treatments were higher than the background value due to the use of phosphate fertilizer. Hg content in soil depth (0--40 cm) was affected more by long-term different fertilization than the underlying soil (40--60 cm). Hg transferred downwards mainly in soil and accumulated in subsurface soils (20--40 cm) continually, which may hide the ecological risk of Hg. Hg content in soil was mainly affected by phosphate and organic matter fertilizers as well as irrigation water, but less affected by nitrogenous or potassium fertilizers, and the use of phosphorus fertilizer was the major reason which caused the accumulation of Hg in soil.