Foxtail millet (Setaria italica L.) is an important crop in northern China’s arid and semi-arid regions. Frequent spring droughts and limited irrigation facilities often cause poor seed germination due to insufficient soil moisture, threatening food security. The irrigation-sowing technique, which creates a localized moist microenvironment around seeds, effectively addresses this issue. However, this technique has been poorly studied, and its effects on foxtail millet seed germination remain unclear. To address this, field experiments were conducted using a two-factor split-plot design, with three drought levels and five irrigation gradients. The results showed that irrigation-sowing increased soil moisture, promoted root–shoot growth coordination, and improved germination characteristics. Transcriptome analysis of seeds under moderate drought compared the optimal irrigation treatment (13.5 m³·hm⁻²) with the non-irrigated control (0 m³·hm⁻²), identifying 2169 differentially expressed genes. Seeds receiving irrigation exhibited higher transcript abundance in pathways related to carbohydrate metabolism, energy production, secondary metabolism, and hormone signaling. Physiological measurements further showed increased α/β-amylase activity, while starch, sucrose, and cellulose content decreased. Glycolytic enzyme activity was enhanced, and ATP content increased by 125%. Additionally, phenylpropanoid metabolism was promoted, and proanthocyanidin accumulation increased by 11.5%. Hormone analysis showed that the contents of IAA and GA increased as germination progressed by 29.09% and 54.70%, respectively, while ABA content decreased. Overall, irrigation-sowing serves as an upstream moisture signal that reshapes metabolic and hormonal states associated with improved germination performance.