<p>Drought has become a serious threat to food security and sustainable development. Studying the mechanism of drought tolerance of plants is crucial to develop drought-tolerant crops, which helps to address food security. This study aimed to explore the metabolic pathways associated with drought tolerance in foxtail millet (<i>Setaria italica</i> L.). The roots of drought-tolerant millet variety Zhonggu2 and the common variety An04 were selected for a comparative analysis of the changes in growth, ions, differentially expressed genes and metabolites between the two accessions in response to drought by transcriptomics and metabolomics. Under drought conditions, the root length of both varieties increased significantly (‘Zhonggu2’ &gt; ‘An04’). The contents of K⁺, Ca²⁺ and NO₃⁻ in Zhonggu2 increased significantly. In phospholipid metabolism, the phospholipase D genes were down-regulated and the contents of inositol and ethanolamine were increased in Zhonggu2. The relative contents of glycine and serine were increased, and the gene encoding serine hydroxymethyltransferase in glycine–serine metabolism were upregulated. In flavanone metabolism, the contents of tyrosine, coumaric acid, naringenin-7-<i>O</i>-glucoside, ferulic acid and vanillic acid were increased and the expression levels of genes encoding 4-coumarate-CoA ligase and shikimate-<i>O</i>-hydroxycinnamoyltransferase were upregulated in the Zhonggu2. Integrated analyses showed that Zhonggu2 prevented the accumulation of reactive oxygen species by promoting glycine–serine metabolism and flavanone metabolism, thereby improving drought resistance. At the same time, Zhonggu2 may also delay the phospholipid decomposition, thereby maintaining the stability of the plasma membrane under drought stress. This study provides important insights for breeding, laying the foundation for future crop genetic improvement.</p>