Drought has gradually become one of the most severe abiotic stresses in plants. A growing body of evidence indicates that stress memory does exist in plants and can improve the plants’ stress resistance. In this study, a total of 195 candidate drought memory-related miRNAs were identified according to the miRNA sequencing data, and targets of 64 (32.8%) candidate miRNAs were validated by degradome sequencing. Several miRNAs like tae-miR408_L-1, tae-miR171a, tae-miR164a-5p, tae-miR396c-5p, tae-miR9778, tae-miR408_L-1, tae-miR9676-5p, tae-MIR9676-p3_1ss21GA, tae-miR9662a-3p and PC-3p-5049_3565 were validated crucial in drought memory. Besides, our results revealed that drought memory displayed a transcriptional stress memory. It could regulate auxin-activated signaling pathway, calcium-transporting, heavy metal transporting, glutathione biosynthetic, protein modification, electron transport, energy metabolism, amino acid metabolism, plant growth and development to respond to the drought. Furthermore, miRNAs may regulate various plant hormones and glucose metabolism pathways to indirectly regulate proline homeostasis and further increase the drought resistance of drought training plants. In addition, the mTOR signaling pathway was also found crucial in drought memory. Our results contribute to an understanding of drought memory in wheat seedlings and may lead to new strategies for drought-resistant breeding.