Atmospheric deposition has become one of the main sources of heavy metals in crops in developed and industrial zones in China for the past several years. However, lack of data of the agro-ecosystems on the vast areas of China makes it difficult to assess the impacts of air pollution on the heavy metal accumulation in crops. In this study, with deposit samples from 67 sites located at different agro-ecosystems (typical, factory nearby, town nearby, roadside, and remote) of four natural regions [Huanghuai (HH), Southeast (SE), Southwest (SW) and upper-mid Yangzi River (Up-mid YR)], atmospheric heavy metal deposition in agro-ecosystems on a large scale in China was studied. The results showed that during the growing season, the deposition fluxes of Cr, Ni, As, Cd, and Pb in typical agro-ecosystems were 0.60-36.86, 0.65-25.37, 0.05-8.88, 0.12-5.81, and 0.43-35.63 μg m day, respectively, which varied greatly between the four different regions. The average deposition fluxes of Cr, Ni, Cd, and Pb in the HH region, as well as the fluxes of As in the SW region, were significantly higher than those in the SE region. Heavy metal deposition rates among agro-ecosystems were very similar, except for the sites around cement factory in flat HH region. In mountainous SW region, however, deposition rates varied widely with sites nearby towns relatively higher and remote regions much lower. Higher correlation coefficients were observed between Cr, As, Pb, and Ni deposition rates, suggesting that they had similar sources. Samples from the SW and SE regions exhibited higher Pb/Pb and Pb/Pb ratios than those from the HH and Up-mid YR regions. Airborne Pb in SW agro-ecosystems were mainly derived from vehicle exhaust and local smelting, whereas that in the HH region from burning of northern Chinese coal.