Research on high-quality Atractylodes chinensis (DC.) Koidz. germplasm is pivotal for its standardized cultivation, but the multi-omics mechanisms governing its plant architecture remain unclear. In this study, we integrated morphological quantification, RNA sequencing (RNA-seq), and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to explore the molecular basis of architectural differences between a naturally compact line (JC) and the wild-type (WT). Morphological analysis confirmed that the JC line is characterized by significantly shorter internodes and increased branching compared to the WT. Transcriptomic analysis identified 7,271 differentially expressed genes (DEGs), specifically the downregulation of the gibberellin (GA) biosynthetic gene ent-kaurenoic acid oxidase ( KAO ) and the upregulation of the GA catabolic gene GA 2-oxidase ( GA2ox ) in the JC line. Parallel metabolomic profiling identified an accumulation of GA metabolic precursors (GA ₉ , GA ₁₉ , and GA ₄₄ ) and significantly higher cytokinin (CTK) content in JC relative to WT. These results suggest a GA-centric regulatory network where disrupted GA metabolism and enhanced CTK accumulation synergistically drive the compact architectural phenotype. This study elucidates the GA–CTK regulatory module as a core mechanism modulating internode elongation and branching, providing key candidate genes and foundational insights for the molecular breeding of elite A. chinensis germplasm.