Transcriptome sequencing was performed on the daughter root of Aconitum carmichaelii （DR） to explore the underlying molecular mechanism regulating the root expansion. DR at three time points during the expansion stages， namely S1 （1 d）， S2 （31 d） and S3 （61 d）， were harvested for sequencing. The identified differentially expressed genes （DEGs） were validated by real-time quantitative polymerase chain reaction （qRT-PCR）. 73600 unigenes were obtained via de novo assembly， including 7555 DEGs that are differentially expressed by comparative transcriptome analysis. There were 2560， 2171 and 6320 DEGs in the three pair-wise comparison groups of S2/S1 （S2 with respect to S1）， S3/S2 （S3 with respect to S2）， S3/S1 （S3 with respect to S1）， respectively. KEGG enrichment analysis showed that DEGs were mainly involved in starch and sucrose metabolism， plant hormone signal transduction， plant-pathogen interaction and phenylpropane biosynthesis. The genes in starch biosynthesis pathway were up-regulated and these genes in lignin biosynthesis were down-regulated， which was considered as a sign in the root expansion. The genes related to auxin， abscisic acid， cytokinin and gibberellin were involved in regulating the process of enlargement. Through testing a subset of candidate genes in these pathways using qRT-PCR， a pattern similar to that revealed by transcriptome sequencing was revealed. 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 clues for further research on the molecular mechanism of DR.