Molybdenum (Mo) is an essential nutrient for leguminous plants, but the effects of Mo exposure on plant growth, especially in relation to soil microorganisms, are not fully understood. This study employed alfalfa (Medicago sativa L.) to evaluate the physiochemical responses to gradient soil Mo variations and explore the potential regulatory role of rhizosphere microorganism - arbuscular mycorrhizal fungi (AMF) in modulating Mo's impact on plant physiology, with a focus on metabolic pathways. The results showed that Mo exerted hormetic effect (facilitation at low doses; inhibition at high doses) on alfalfa growth, promoting biomass (below 90.94 mg/kg, with a 63.98 % maximum increase), root length (below 657.11 mg/kg, with a 39.29 % maximum increase), and plant height (below 304.03 mg/kg, with an 18.4 % maximum increase). Excess Mo (1000 mg/kg) resulted in a reduction in photosynthesis and biomass growth due to increased oxidative stress (p < 0.05). Within the stimulatory zones, AMF enhanced Mo accumulation in alfalfa, augmenting its phytological effects. Exceed the stimulatory zones, AMF enhanced alfalfa Fe uptake and reduced the generation of reactive oxygen species (ROS) induced by excess Mo by shifting the redox homeostasis-controlled enzyme from peroxidase (POD) to superoxide dismutase (SOD), thereby improving alfalfa's tolerance to Mo. Metabolomic analysis further revealed that AMF promoted the biosynthesis of indole acetic acid (IAA) and various amino acids in Mo-stressed alfalfa (p < 0.05), which accelerated alfalfa growth and mitigated Mo-induced phytotoxicity. These insights provide a foundation for developing sustainable management strategies for Mo-exposed soils using AMF inoculants, such as minimizing Mo fertilizer application in Mo-deficient soils and facilitating the reclamation of Mo-contaminated soils.