Arbuscular mycorrhizal fungi (AMF) are ubiquitous in farmland. But the knowledge on AMF impact on lead (Pb) migration in farmland is limited. A field experiment was conducted in the rainy season (May–October) for two years in a Pb-polluted farmland. Benomyl was used to specifically suppress the native AMF growth in the farmland. The effect of benomyl-induced AMF suppression on the Pb uptake in maize, and Pb loss via surface runoff and interflows (20 cm and 40 cm depth) from the farmland was investigated. The benomyl significantly inhibited the AMF growth, resulting in decreases in the colonization rate, spore number, and contents of total and easily extractable glomalin-related soil protein (GRSP); and promoted the Pb migration into maize shoots and mainly enriched in leaves. The particulate Pb accounted for 83.2%–90.6% of Pb loss via surface runoff, while the proportion of particulate Pb loss via interflow was decreased and the proportion of dissolved Pb loss increased with the increase of soil depth. The AMF suppression led to a decrease in dissolved Pb concentration and loss, but an increase in particulate Pb concentration and loss, and enhanced the total Pb loss via surface runoff and interflows. Moreover, significant or very significant negative correlations were observed between the AMF colonization rate in roots with the Pb uptake in leaves, and the content of easily extractable GRSP with the particulate Pb loss. These results indicated the native AMF contributed to immobilizing Pb in soil and inhibited its migration to crops and the surrounding environment.