Sweet sorghum (Sorghum bicolor Moench) seedling emergence and growth are significantly impeded by physical soil crusts (PSCs) in saline-alkaline soils. Abscisic acid (ABA) is a potent seed priming agent known for modulating plant physiological and metabolic responses under salinity stress. However, the influence of ABA priming on seedling emergence in PSCs remains unclear. This study conducted both pot and field experiment to examine the effects of ABA priming on enhancing seedling emergence under PSC conditions. ABA priming altered the balance of at least 24 endogenous phytohormones, including abscisic acid, jasmonic acid, gibberellins, ethylene, auxins, and cytokinins. Additionally, it reprogrammed starch and sucrose metabolism, resulting in the differential expression of genes encoding key enzymes such as AMY, BAM, and INV, which are crucial for converting complex sugars into readily available energy sources, thereby supporting seedling growth. Furthermore, 52 differentially expressed metabolites (DEMs) of flavonoids were identified in germinating seedlings, including 15 anthocyanins, 3 flavones, 7 flavonols, 6 isoflavones, 7 flavanones, and 14 other flavonoids. Genetic and metabolic co-expression network analysis, along with flavonoid biosynthesis pathway exploration, revealed that the biosynthesis of 17 key DEMs-including liquiritigenin, apigenin, kaempferide, syringetin, phloretin, formononetin, dihydrokaempferol, and xanthohumol-was regulated by 10 differentially expressed genes (DEGs) associated with flavonoid biosynthesis. These DEGs encoded 7 enzymes critical for this pathway, including chalcone synthase, shikimate O-hydroxycinnamoyltransferase, bifunctional dihydroflavonol 4-reductase, naringenin 7-O-methyltransferase, and anthocyanidin reductase. This regulation, along with reduced levels of superoxide anion (O2-) and malondialdehyde and increased antioxidant enzyme activities, suggested that flavonoids played a vital role in mitigating oxidative stress. These findings demonstrate that ABA priming can effectively enhance sweet sorghum seedling emergence in PSCs by accelerating emergence and boosting stress resistance.