Drought, salinity, extreme temperatures, pathogens, and attacks by herbivores are environmental stresses that plants experience repeatedly. In order to survive in repeated stressful environments, plants have evolved a new adaptive mechanism known as ‘stress memory’. Coordinated responses of cell, gene/genome, and epigenetic modifications, including altered physiological responses, gene activation, hyper-induction and chromatin modification are considered necessary for the formation of stressed memories. Cotton ( Gossypium spp.) is an important economic crop, which can be used as raw materials in many fields and has high economic value. Here, we ensured that G. hirsutum drought memory was established after cycles of mild drought and re-watering treatment, and studied gene expression by whole-transcriptome RNA sequencing. The physiological, biochemical and molecular mechanisms of drought stress memory formation in G. hirsutum were revealed. As a histone modification, H3K4me3 plays an important role in [+/+] transcript memory. In addition, the intergenerational inheritance phenomenon of drought stress memory in G. hirsutum was also exhibited. Our results showed that the pathways of long-term and short-term memory may be different.