Drought stress during sorghum emergence significantly impacts seedling establishment, with drought adversely affecting both emergence and population growth. This study aims to explore drought tolerance mechanisms in sorghum germination by analyzing physiological changes and transcriptomic data from two sorghum lines: W069 (drought-tolerant) and W040 (drought-sensitive). Under drought conditions, phenotypic analysis revealed that W069 exhibited longer shoot and root lengths compared to W040. Additionally, physiological data indicated higher osmotic substance content and lower MDA content in W069. Through Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, three key pathways (starch and sucrose metabolism, phenylpropanoid biosynthesis, and phytohormone signaling) were identified as pivotal in drought response during seed germination in sorghum. Expression profiling revealed that most of the drought tolerance-related genes in the three key pathways were expressed at higher levels, in the drought-tolerant cultivar 'W069', which may be the reason for its greater stress tolerance. These findings enhance our comprehension of drought-responsive gene networks in sorghum seed germination, offering potential target genes and strategies for enhancing drought tolerance in this crop.