The leaves and roots of Sarcandra glabra (thunb) nakai have different therapeutic effects in some clinical applications. In order to explore the tissue specific distribution differences of terpenoids in the leaves and roots of S. glabra, and to analyze the molecular mechanism of the formation of their pharmacodynamic quality differences. In this study, liquid chromatography-mass spectrometry (LC-MS) and Illumina HiSeq^TM high-throughput sequencing techniques were respectively used to obtain the metabolome and transcriptome data of the leaves and roots of S. glabra. The metabolomics analysis showed that there were 50 differential terpenoids metabolites between the leaves and roots, including farnesylcysteine, d-glyceraldehyde 3-phosphate, and (R)-5-phosphomevalonate. The transcriptomics analysis indicated that there were 57 differentially expressed metabolic enzyme coding genes, including ACTC, HMGCR, MVK, DXS, and KS. Moreover, there were seven transcription factors, including MYB, C2H2, AP2/ERF-ERF, which were predicted to participate in regulating the differences in terpenoid synthesis and accumulation between the leaves and roots of S. glabra. qRT-PCR results demonstrated that the expression changes of eight randomly selected enzyme genes involved in terpene synthesis between the leaves and roots of S. glabra, which were consistent with the transcriptome sequencing results. This study will help to elucidate the molecular mechanisms underlying the clinical efficacy differences between the leaves and roots of S. glabra, and facilitate the extraction, utilization, and resource development of S. glabra.