【Objective】This study aimed to investigate the input and output characteristics of cadmium (Cd), copper (Cu), and lead (Pb) in different atmospheric deposition areas.【Method】The arable soils (0-20 cm) of Guixi Smelter with main wind direction at 34 km (background site), 6 km (moderate deposition site) and 1 km (high deposition site) were selected as the research objects. The main input (atmospheric deposition, irrigation water, pesticides, and fertilizers) and output pathways (surface runoff, leaching water, and grain harvest) were monitored and quantitatively analyzed for three years by using the chemical mass balance (CMB) method.【Result】The results showed that the average annual input fluxes of Cd in the background, moderate, and high deposition sites by atmospheric deposition were 0.84, 2.26, 9.01 mg?m-2?a-1, accounting for 43.18%, 38.33%, and 100%, while the average annual input fluxes of Cu were 17.62, 99.68, 747.6 mg?m-2?a-1, accounting for 80.76%, 86.24%, 100%, respectively. Also, the average annual input fluxes of Pb were 13.93, 27.43, 73.17 mg?m-2?a-1, accounting for 97.75%, 92.36%, and 100%, respectively. Specifically, the average annual input fluxes of Cd in the background and moderate deposition sites due to irrigation water were 1.05 and 3.60 mg?m-2?a-1 and accounted for 54.62% and 60.82%, respectively, whereas the annual heavy metal input fluxes by pesticides and fertilizers accounted for less than 5%, which could be ignored. The main output pathways of arable soil in different atmospheric deposition areas were surface runoff and leaching water, with the output ratio ranging from 86.66% to 100%, and the output ratio of the grain harvest ranging from 2.88% to 13.34%. From 2019 to 2021, the average annual net input fluxes of Cd, Cu, and Pb were all greater than 0 in the background site, moderate deposition site, and high deposition site. For example, the average annual net input fluxes of Cd were 1.54, 1.96, and 4.38 mg?m-2?a-1, for Cu were 12.72, 28.02, and 184.0 mg?m-2?a-1, and for Pb were 13.03, 21.31, 55.04 mg?m-2?a-1 in the background site, moderate deposition site, and high deposition site, respectively. 【Conclusion】In general, it is advisable to strengthen the long-term supervision of atmospheric pollution sources and irrigation water quality in the study area and avoid the direct return of straw to the field. This study provided theoretical support for the remediation of heavy metal pollution and the protection of environmental quality in regional arable soils.