Abstract: Six typical pear orchards with different fertilization methods (traditional farmyard manure, chemical fertilizer and commercial organic fertilizer) in both plain and hilly regions of the northwesthern Zhejiang province were selected to study the flows of Zn, Cu, Pb, Cd, Hg, and As loaded by organic manure, chemical fertilizers, atmospheric deposition, pear harvest, and surface runoff in pear production system through one-year field monitoring. The annual mass balance values of the heavy metals in the orchard production system and their influencing factors were also discussed. The results showed that balance values of heavy metals of the orchard from plain region were higher than those from hilly region. And the input contribution of heavy metals from atmospheric deposition in the plain region was higher than those in the hilly region. Annual accumulation of most of the heavy metals was the highest for the orchard applied with the organic fertilizer. Cd in the orchard was mainly from chemical fertilizer, meanwhile Zn, Cu and Pb in the orchard were mainly from organic fertilizer. The atmospheric deposition also contributed greatly to the accumulation of Zn, Pb, Hg, and As in the orchard. In the hilly region, for the orchard with applied with traditional farmyard manure, Pb and As were slightly accumulated, and other heavy metals showed decrease trend. For the orchard with applied with chemical fertilier, Pb, Cd and As were accumulated, while Zn, Cu and Hg showed decrease trend. For the orchard with applied with commercial organic fertilizer, all of the heavy metals were accumulated with the highest, especially for Zn. Heavy metals in orchards of plain region, except for Cu under conventional fertilization patterns, and Zn and Cu in chemical fertilizer, showed accumulation trend. This was due to more input of heavy metals from atmospheric deposition.