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Garlic has a strong ability of selenium (Se) accumulation and is one of the best target crops for Se biofortification. Arbuscular mycorrhizal fungi (AMF) inoculation might enhance the nutritional qualities and the absorption ability of exogenous Se in plants. However, little is known about the exogenous Se application and AMF inoculation on garlic. Here, we evaluated the effects of different concentrations of exogenous Se on the growth, nutritional quality, and selenium enrichment of garlic. The results demonstrated that significantly higher Se content of garlic bulb was found in exogenous Se treated plants, and the Se accumulation was improved with the increasing of Se supply. Low application of exogenous Se appreciably improved the yield and the contents of soluble sugar and allicin in garlic bulbs, but the opposite was observed at high Se concentration. Furthermore, AMF inoculation significantly reduced the inhibition effect of high concentration Se on garlic. AMF supply was effective in improving the growth and nutritional indicators of garlic, which promoted the exogenous Se utilization rate when combined with 10 mg/L exogenous Se treatment. The results will provide a more theoretical basis for the production of high-quality selenium enrichment garlic.