Heavy metal pollution in farmland soil reduces crop yield and quality and also potentially causes the crisis to human health. Formerly, the fact that silicon fertilizer could effectively reduce the residual concentration of heavy metal in crops has been identified at the tissue level. In this paper, molecular dynamics simulation was employed to investigate the effects of the degree of silicification of silicic acids [namely, the molar ratio of Si(OH)4 and SiO2] on the Cd(II) bound in the aspect of radial distribution functions and mean square displacements. The results demonstrated that Si(OH)4 attracted Cd(II) through the coordination, while SiO2 attracted Cd(II) by the adsorption. In particular, when the degree of silicification was 0, both the bound Cd(II) amount and strength were the maximum value, indicating that the silicon fertilizer had the best efficiency of Cd(II) bound as Si(OH)4. By comparing the adsorption energy and electronic transfer of Cd(II) and Si(OH)4 adsorption onto the SiO2 surface through the quantum chemical simulation, we concluded that Cd(II) adsorption onto the SiO2 surface was chemisorption, while the Si(OH)4 adsorption onto SiO2 surface was physisorption. Consequently, the adsorption capacity of Cd(II) on the SiO2 surface was higher than that of Si(OH)4 adsorption on the SiO2 surface. Moreover, the compact hydration layers around Cd(II) prevented the process of Cd(II) adsorption on the SiO2 surface; even so, the counterion Cl- in the system promoted the adsorption process. The mechanism of silicon fertilizer binding heavy metal Cd(II) was investigated and revealed at the molecular and electronic level. This work has expanded the possibility of theoretical guidance for the design of silicon fertilizer.