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Melatonin application has obvious improving effects on alleviating the drought-induced inhibition of plant growth. However, the root phenotypic dynamics in wheat treated with melatonin remain unknown. This study was conducted using RhizoPot, a novel and improvised in situ root observation device, with three treatments, including normal water condition (CK), drought condition (Ds, relative water content 45–50%), and 100 µM melatonin treatment under drought condition (MT). Results showed that MT application effectively improves root morphological indicators, including root (specific root) length, surface area, and volume; root length density; and the average root diameter of wheat plants. Also, the inhibitory effect of drought on shoot morphology, including plant height, dry weight, net photosynthesis, and stomatal aperture of leaves, were improved significantly through MT under drought condition. Life span and percent survival of fine root, lateral root, and root hair at different segments were also effectively improved under MT treatment. Compared with those shown under CK and Ds, the melatonin contents in leaves and roots were increased, and the expression levels of melatonin-synthesis-related genes (TaCOMT and TaTDC) were upregulated significantly under MT treatment. The findings of this study may clarify the drought resistance mechanism of wheat treated with melatonin under drought stress. [ABSTRACT FROM AUTHOR]