Residual pesticides in soil may be taken up by crops and negatively affect food safety. The uptake mechanism of imidacloprid and propiconazole was studied using wheat roots. The factors affecting root uptake were also studied with different crops and in different soils. Imidacloprid and propiconazole were taken up by wheat roots mainly through the symplastic and apoplastic pathways, respectively. Root protein and lipid contents were the main factors affecting the uptake and accumulation of imidacloprid and propiconazole by different crop roots, respectively. The uptake of imidacloprid and propiconazole in soil by wheat plants was linearly correlated with their concentrations in soil pore water, which were governed by soil characteristics. These results are helpful for understanding and estimating crop uptake of residual pesticides in soils.