To investigate the effect of soil arbuscular mycorrhizal fungi (AMF) on Cd migration in contaminated soil–crop system, the farmland soil polluted by heavy metals around the Lanping Lead Zinc Mine in Yunnan Province was used to carry out indoor experiments. The specific fungicide (benomyl) was applied to inhibit indigenous AMF in soil, and the effects of inhibiting AMF on corn growth, Cd content and accumulation, and soil Cd leaching loss were studied. The results showed that the application of benomyl significantly inhibited the growth of soil AMF, resulting in the significant reduction in the infection rate of AMF, the number of spores, and the content of soil glomalin related soil protein (GRSP); It also significantly affected the growth and mineral nutrition of maize, leading to the increase in the aboveground biomass, chlorophyll and phosphorus contents in maize, while the decreases in the aboveground nitrogen and potassium contents. The application of benomyl promoted the migration of Cd to the roots and shoots, mainly concentrated in the shoots, resulting in the significant increases in the content and accumulation of Cd in shoots. The application of benomyl resulted in the significant increases in Cd concentration in the 10 cm and 20 cm soil streams. In addition, soil GRSP content was significantly negatively correlated with the accumulation of Cd in the aboveground part of maize and Cd loss concentration in soil subsurface flow. The research results indicated that indigenous AMF in soil can help inhibit the migration of soil Cd to the aboveground parts of plants, reduce the loss concentration of Cd in soil subsurface flow, and reduce the environmental migration of Cd in polluted soil–crop systems.