The optimal treatment designs of the heavy metal pollution sites and the calculation of the recovery capacity are important in recent studies. In this paper, we aimed to model the accumulation of heavy metals under different artificially Cd added concentrations, and analyzed the various tobacco solute adsorption and fluid flow properties. The finite difference method was used to simulate the heavy metals flux and root absorption in the soil, and the model simulation was compared with the measured values to quantify the uncertainty of the metal transport and modeling parameters. Treatments with different Cd levels were compared, e.g., control tillage (CT), low Cd tillage (LT, 2.0 mg/kg), high Cd tillage (HT, 20.0 mg/kg), ultra-high Cd tillage (UHT, 80.0 mg/kg). The predicted soil water content (SWC) was consistent with observed data. Predicted cumulative root water uptake (mm) ranked as follows: CT (196)>LT (178)>HT (134)>UHT (117). Potential transpiration rates (T r p) under HT and UHT were lower than that of other treatment, because of their lower leaf Area Index (LAI). The predicted root Cd uptake showed a strong correlation within the actual Cd uptake. The predicted root absorption of Cdmax was UHT (180.17)> HT (106.52)> LT (53.20) >CT (0.610). However, deviation of models was added by the Cd effluent trend and the performance of root exudates. This finding would be useful for further investigation into bio-remediation in the agricultural area, not only for Cd ion but for a range of other heavy metal contaminants.