Drought stress during sorghum emergence significantly affects seedling establishment, adversely affecting both emergence and population growth. This study investigates drought tolerance mechanisms during sorghum germination by analyzing physiological changes and transcriptomic data from two lines: W069 (drought tolerant) and W040 (drought sensitive). Under drought conditions, a phenotypic analysis revealed that W069 exhibited longer shoots and roots than W040. Additionally, physiological data indicated higher osmotic substance and lower malondialdehyde levels in W069. Using Kyoto Encyclopedia of Genes and Genome analyses, we identified three key pathways (starch and sucrose metabolism, phenylpropanoid biosynthesis, and phytohormone signaling) as pivotal in the drought response during seed germination in sorghum plants. Expression profiling revealed that most drought tolerance-related genes in the three key pathways were expressed at higher levels in the drought-tolerant cultivar W069, possibly explaining its greater stress tolerance. These findings enhance our understanding of drought-responsive gene networks in sorghum seed germination, offering potential target genes and strategies for enhancing drought tolerance in this crop.