Polygonum cuspidatum, an important medicinal plant, is rich in resveratrol and polydatin, but it frequently suffers from drought stress in the nursery stage, which inhibits the plant’s growth, active components concentrations, and the price of rhizome in the later stage. The purpose of this study was to analyze how exogenous 100 mM melatonin (MT) (an indole heterocyclic compound) affected biomass production, water potential, gas exchange, antioxidant enzyme activities, active components levels, andresveratrol synthase(RS) gene expression ofP.cuspidatumseedlings growing under well-watered and drought stress conditions. The 12-week drought treatment negatively affected the shoot and root biomass, leaf water potential, and leaf gas exchange parameters (photosynthetic rate, stomatal conductance, and transpiration rate), whereas the application of exogenous MT significantly increased these variables of stressed and non-stressed seedlings, accompanied by higher increases in the biomass, photosynthetic rate, and stomatal conductance under drought versus well-watered conditions. Drought treatment raised the activities of superoxide dismutase, peroxidase, and catalase in the leaves, while the MT application increased the activities of the three antioxidant enzymes regardless of soil moistures. Drought treatment reduced root chrysophanol, emodin, physcion, and resveratrol levels, while it dramatically promoted root polydatin levels. At the same time, the application of exogenous MT significantly increased the levels of the five active components, regardless of soil moistures, with the exception of no change in the emodin under well-watered conditions. The MT treatment also up-regulated the relative expression ofPcRSunder both soil moistures, along with a significantly positive correlation between the relative expression ofPcRSand resveratrol levels. In conclusion, exogenous MT can be employed as a biostimulant to enhance plant growth, leaf gas exchange, antioxidant enzyme activities, and active components ofP.cuspidatumunder drought stress conditions, which provides a reference for drought-resistant cultivation ofP.cuspidatum.