Drought stress poses a significant threat to global agricultural production, including the cultivation of medicinal plants. Plant growth-promoting bacteria (PGPB) and the eco-friendly element silicon (Si) are known to alleviate the adverse effects of drought stress. This study examines how inoculation with Bacillus pumilus G5 or/and Si influences plant hormone signaling and flavonoid biosynthesis pathways in drought-stressed Glycyrrhiza uralensis Fisch. (G. uralensis), focusing on genetic and metabolic aspects. The results indicate that the combined application of G5 and Si (G5+Si) may regulate the crosstalk among jasmonate (JA), gibberellin (GA), and ethylene (ET) signaling pathways, thereby up-regulating key flavonoid biosynthesis genes, including phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate-CoA ligase (4CL), and chalcone synthase (CHS), leading to the accumulation of isoliquiritigenin, liquiritigenin, liquiritin, and licochalcone A, thereby enhancing the drought tolerance of G. uralensis seedlings. The findings provide new insights into the synergistic role of PGPB and Si in improving plant resilience to drought stress, offering theoretical reference for further studies on plant drought tolerance mechanisms.