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<i>Acanthopanax senticosus</i> (<i>A. senticosus</i>) is a member of <i>Acanthopanax Miq.</i> and is used in traditional Chinese medicine, and it has been found that grafting technology can be used to alter plant metabolite composition and transcriptome characteristics. In this study, shoots of <i>A. senticosus</i> were grafted onto the rootstocks of the vigorous Acanthopanax sessiliflorus (<i>A. sessiliflorus</i>) to improve its varietal characteristics. In order to investigate the changes in metabolites and transcriptional patterns in grafted <i>A. senticosus</i> leaves (GSCL), fresh leaves were collected from 2-year-old grafted <i>A. senticosus</i> scions, while self-rooted seedling <i>A. senticosus</i> leaves (SCL) were used as controls to analyse the transcriptome and metabolome. Metabolic profiles and gene expression patterns were further identified and correlated in special metabolite target pathways. The content of chlorogenic acid and triterpenoids in the GSCL was higher than in the control, while the quercetin content was lower. All these metabolic changes were associated with changes in the expression pattern of transcripts. Our results revealed the transcriptome and metabolome characteristics of GSCL. This may help to improve leaf quality in <i>A. senticosus</i> cultivation, suggesting that it is feasible to improve the medicinal quality of GSCL through asexual propagation, but the long-term effects need further investigation. In conclusion, this dataset provides a useful resource for future studies on the effects of grafting on medicinal plants.