Transcriptome sequencing was performed on the daughter root of Aconitum carmichaelii (DR) to explore the underlying molecular mechanism regulating the expansion of DR. DR from three time points during the expansion stages, namely S1 (1 D), S2 (31 D) and S3 (61 D), were selected for sequencing. The related differential genes were verified by real-time quantitative polymerase chain reaction (qRT-PCR). 73600 Unigenes were obtained; 7555 differential expression genes (DEGs) were obtained by comparative transcriptome analysis. There were 2560, 2171 and 6320 DEGs in the three comparison groups of S2vS1, S3vS2 and S3vS1, respectively. More down-regulated DEGs were indicated than the up-regulated; KEGG enrichment analysis showed that DEGs were mainly involved in starch and sucrose metabolism, plant hormone signal transduction, plant-pathogen interaction and phenylpropane biosynthesis. Starch biosynthesis pathway was up-regulated and lignin biosynthesis was down-regulated, the auxin and abscisic acid signaling pathway was up-regulated while the cytokinin and gibberellin signaling pathways were down-regulated; these pathway-related genes were performed in regulating the process of enlargement. The genes involved in these pathways were screened for qRT-PCR. The results were consistent with the expression patterns of transcriptome data which indicates the data obtained by transcriptome sequencing is reliable. This study is the first to explore the dynamic transcriptional changes in the process of DR enlargement, and excavate the related genes involved in the regulation of the enlargement process, which provides information for improving the yield of DR and provides clues for further research on the molecular mechanism of DR.