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BACKGROUND: The active component content is an important factor affecting quality of traditional Chinese medicines. The fume‐drying process can effectively improve the content of active components in rhubarb, but the accumulation dynamics and molecular mechanisms are not known. In this study, variations in the active components of rhubarb during the drying process were determined, and the most intense changes in the active components were preferred for transcriptome inquiry. RESULTS: The results showed that the accumulation of active ingredients could be significantly promoted in the early stage of fume‐drying and air‐drying. In particular, the active ingredients increased by 61.57% (from 44.58 to 72.02 mg g−1) on the fourth day of fume‐drying. A total of 4191 DEGs (differentially expressed genes) were identified by transcriptome analysis when the active components changed significantly. Transcriptome data of different dried rhubarb samples revealed, that the fume‐drying process could significantly improve the expression of genes relevant to respiration, phenolic acid, and anthraquinone synthesis pathways in rhubarb, which was more conducive to the synthesis and accumulation of the active components. CONCLUSION: Fume‐drying stimulated respiration and secondary metabolite synthesis in rhubarb cells by exerting strong external stress on freshly harvested rhubarb. This study revealed the variations and molecular mechanism of active component accumulation in the rhubarb drying process and might serve as a guide for the development of alternative methods for rhubarb fumigation and drying process. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]