Vegetation degradation induced by rare earth element (REE) mining, combined with intense rainfall, markedly enhances runoff generation and associated contaminant transport, posing persistent risks to soil stability in mined landscapes. Arbuscular mycorrhizal fungi (AMF) play a crucial role in regulating soil structure and hydrological processes, yet their responses to contrasting REE mining practices and their contribution to runoff regulation remain poorly constrained. In this study, we examined the responses of AMF community to heap leaching (HL), in situ leaching (IL), and ecological restoration (ER) in REE mining areas, and further quantified the effects of indigenous AMF communities on runoff generation under simulated rainfall. Heap leaching resulted in severe soil desertification, whereas in situ leaching primarily induced soil acidification that is assessed based on soil pH. Relative to original ores (OR), HL significantly reduced AMF abundance and diversity and caused pronounced shifts in community composition. Ecological restoration partially recovered AMF abundance, Chao 1 and observed species, but did not restore them to reference levels, while IL also induced marked alterations in AMF community structure. Variations in AMF communities across mining sites were mainly explained by soil clay content, nutrient availability, and precipitation. Rainfall simulation experiments suggest that inoculation with indigenous AMF communities significantly reduced runoff from degraded tailing sands partially by enhancing soil binding agents and promoting plant growth. These findings identify AMF as an important, yet often overlooked, biological regulator of runoff generation in REE mining landscapes, and suggest that reestablishing native AMF communities represents a viable nature-based strategy for mitigating erosion and improving the hydrological functioning of disturbed soils.