In this study, the positive role of putrescine in alleviating the negative impact of drought stress on morphological and biochemical indices of indigo seedling was investigated. This experiment was carried out as a factorial experiment based on a completely randomized design with five replications. Four seeds of Indigofera tinctoria sowed in 4.5 L pots. The plants sprayed with putrescine (0, 0.5, and 1 mM) at 5th week after planted and then were applied severe, moderate, low, and normal drought stress (25, 50, 75, and 100% FC, respectively). Moderate and severe drought stresses significantly reduced the amount of chlorophyll a, total chlorophyll, ratio of chlorophyll a/b, relative water content, and protein compared with the control. Putrescine reduced the adverse effects of drought stress on the fresh and dry weight of roots and shoots, root length and leaf area, dry matter, relative water content, and protein. Drought stress increased the amount of chlorophyll b, carotenoids, accumulation of soluble sugars in roots and proline in roots and shoots, reactive oxygen specious, peroxidase enzyme activity, and amount of anthocyanin in leaves. The putrescine treatment significantly reduced the amount of ROS and enzyme activity in moderate and severe drought stress compared to untreated plants with putrescine. In general, foliar spraying of indigo plants with 0.5 mM putrescine improved the vegetative state of plants by improving the antioxidant system against oxidative stress, especially under the moderate and severe drought stress conditions, and increased dry matter by 43% under the moderate drought stress.