Atmospheric deposition of heavy metals is widely documented and has been connected to adverse ecological and health impacts. The influence of atmospheric deposition on the soil-rice system in a typical urban agglomeration region was studied continuously through a field contrast experiment for two years. The results showed that the Cd and Pb in rice grains is mainly from soil, but Cd and Pb from the atmospheric deposition should be a focus of attention. The bioavailable content of heavy metals in atmospheric deposition is higher than that in corresponding surface soil. Atmospheric deposition contributed 10.8-47.7% of the Cd and Pb in brown rice, and 13.7-60.3% of the Cd and Pb in rice leaves was from atmospheric deposition. In the traffic area, a high deposition site, the contributions of atmospheric depositions to heavy metals in rice plants were higher than those from abandoned mine area and suburban area. Atmospheric deposition also consistently decreased the pH (0.17-0.66) and increased the exchangeable Cd (27.1-62.1%) and Pb (3.3-26.1%) in surface soil. In addition, the health risk index (HRI) of rice consumption was also increased as a result of the different atmospheric depositions of heavy metals, which accounted for 40.0% and 35.5% of Cd and Pb at the high deposition site, respectively. These findings demonstrate the potential influences of atmospheric deposition on the soil-crop system and human health, and can also provide a useful reference for developing the emission control strategies.