In this study, the role of exogenous root exudates and microorganisms was investigated in the application of modified nanoscale zero-valent iron (nZVI) for the remediation of cadmium (Cd)-contaminated soil. In this experiment, citric acid (CA) was used to simulate root exudates, which were then added to water and soil to simulate the pore water and rhizosphere environment. In detail, the experiment in water demonstrated that low concentration of CA facilitated Cd removal by nZVI, while the high concentration achieved the opposite. Among them, CA can promote the adsorption of Cd not only by direct complexation with heavy metal ions, but also by indirect effect to promote the production of iron hydroxyl oxides which has excellent heavy metal adsorption properties. Additionally, the H+ dissociated from CA posed a great influence on Cd removal. The situation in soil was similar to that in water, where low concentrations of CA contributed to the immobilization of Cd by nZVI, while high concentrations promoted the desorption of Cd and the generation of CA–Cd complexes which facilitated the uptake of Cd by plants. As the reaction progressed, the soil pH and cation exchange capacity (CEC) increased, while organic matter (OM) decreased. Meanwhile, the soil microbial community structure and diversity were investigated by high-throughput sequencing after incubation with CA and nZVI. It was found that a high concentration of CA was not conducive to the growth of microorganisms, while CMC had the effect of alleviating the biological toxicity of nZVI.