Bud dormancy is a key adaptive strategy in perennial plants, enabling them to survive adverse environmental conditions. However, it poses challenges in crop cultivation, especially in fruit crops such as apple, in which synchronized bud break is crucial for consistent growth and yield. The synthetic cytokinin 6-benzylaminopurine (6-BA) promotes dormancy release; however, its molecular and metabolic mechanisms remain largely unclear. This study investigates dormancy release in nursery-grown Xianheng 01 apple rootstocks through integrated transcriptomic, metabolomic, and hormonal analyses. Dormant buds were treated with 6-BA, with morphological, biochemical, and molecular profiling performed over 30 d. 6-BA treatment increased plant height and leaf emergence by increasing the levels of cytokinins (DHZR, IPA) and decreasing the level of abscisic acid (ABA). Transcriptomics analysis identified 7,009 differentially expressed genes (DEGs) in response to 6-BA treatment. The cytokinin-responsive gene A-ARR8 exhibited a distinct expression pattern, being upregulated at 1, 3, and 6 d post-treatment but downregulated at 11 d. In contrast, ABA-related genes SnRK2a/b, PP2C, and ABF3, were consistently downregulated throughout the treatment period. Metabolomic analysis identified 2,053 metabolites, showing early-phase dominance of phenylpropanoids, and flavonoids, followed by a shift towards ABC transporter-mediated nutrient mobilization. Conjoint analysis highlighted the coordinated activation of secondary metabolite biosynthesis and cytokinin signaling. These results demonstrate that 6-BA induces dormancy release through cytokinin–ABA antagonism and phased metabolic reprogramming from stress defense to growth promotion. Our findings provide a comprehensive framework for optimizing dormancy management in apple cultivation and highlight 6-BA as an effective agrochemical for improving temperate fruit production.