Mirabilis himalaica is a Tibetan medicinal plant whose tuberous root is its principal medicinal organ. To characterise molecular and metabolic differences associated with root enlargement, we integrated untargeted metabolomic and transcriptomic analyses of enlarged and non-enlarged roots. We identified 1465 metabolites, including 336 differentially accumulated metabolites, and 4058 differentially expressed genes. Flavonoids and phenolic acids were predominantly less abundant in enlarged roots, whereas several alkaloids showed higher relative abundance. Three gibberellin-related metabolites were lower in enlarged roots, while 1-Aminocyclopropanecarboxylic acid (ACC), L-tryptophan, tryptamine, and several cytokinin-related metabolites showed higher relative signals. Tryptophan metabolism was a shared enriched pathway in the integrated analysis. L-Tryptophan was positively correlated with Anthranilate synthase beta subunit 2 (ASB2) and negatively correlated with Tryptophan synthase alpha chain (TSA) and Probable indole-3-pyruvate monooxygenase (YUC) across the six samples; these exploratory correlations do not establish regulatory relationships. The observed patterns are consistent with coordinated changes in hormone-related metabolites, secondary metabolism, and gene expression during root enlargement. Because Indole-3-acetic acid (IAA) and lignin were not directly quantified, the study does not infer their concentrations or deposition. These findings provide a multi-omics resource for investigating tuberous-root development and for guiding future functional and targeted validation studies in this endangered medicinal species.