Heavy metal accumulation in agricultural products has become a major concern. Previous studies have focused on the transport of heavy metals from the soil and their accumulation in crops. However, recent studies revealed that wheat leaves, ears, and awns can also transport and accumulate heavy metals. Wheat grains can be influenced by two sources of heavy metals: soil contamination and atmospheric deposition. To comprehend the transport characteristics of heavy metals in soil, atmospheric deposition, and wheat, 37 samples each for wheat rhizosphere soil, wheat roots, stems, leaves, and grains were collected. Fifteen samples of atmospheric dry deposition and atmospheric wet deposition were collected from Linshu County (northern area), China. Based on the test data, the characteristics of heavy metals and their distribution in the study area were analyzed. Migration patterns of heavy metals in crops from different sources were investigated using Pearson correlation and redundancy analysis. Finally, a predictive model for heavy metals in wheat grains was developed using multiple linear regression analysis. Significant disparities in the distribution of heavy metals existed among wheat roots, stems, leaves, and grains. The coefficient of variation of heavy metals in atmospheric deposition was relatively high, indicating discernible spatial patterns influenced by human activities. Notably, a positive correlation was observed between the concentration of heavy metals in wheat grains and atmospheric deposition of Hg, Cd, and Pb. Conversely, Zn and Ni levels in wheat grains were significantly negatively associated with soil Zn, Ni, pH, and OM content. The contribution of heavy metal elements from different sources varied in their impact on the grain's heavy metal content. Specifically, atmospheric deposition was the primary source of Hg and Pb in wheat grains, while Cd, Ni, Cu, and Zn were predominantly derived from soil. Using a multiple linear regression model, we could accurately predict Hg, Pb, Cd, Ni, Zn, and As concentrations in crop grains. This model can facilitate quantitative evaluation of ecological risk of heavy metals accumulation in crops in the study area.