According to the major differences of agricultural characters among various Aconitum carmichaelii cultivars, the lateral roots of Ai-leaf and Dahua-leaf A.carmichaelii plants were selected as the research objects. And the Illumina Hiseq high-throughput platform was used for transcriptome sequencing, assembly and annotation. We mostly focused the activity differential transcripts, metabolism pathways and enrichment functions. The results showed that a total of 52.23 Gb nucleotide bases were obtained from 6 A.carmichaelii transcriptome databases, with 52 471 unigenes and 28 765 matched annotation. There were 1 052 transcripts of the two kinds of A.carmichaelii with a difference of more than 2 times, 808 of which were annotated. Through GO and COG analysis, they were found to mainly concentrate in metabolic processes, cell processes, catalytic processes and transport processes, connections and other functions. KEGG analysis showed that 262 DEGs were enriched in 78 metabolic pathways, such as starch and sucrose metabolism, plant hormone signaling, carbon compounded transport etc. It was implied that many genes in Dahua-leaf A.carmichaelii regulated the conversion of starch to small molecules such as sucrose, glucose and maltose, while some other genes regulated the accumulation of amino acids, which may be the important biological principles for the formation of the differences between the quality and disease resistance of two leaf types of A.carmichaelii. This study will provide reference datas for A.carmichaelii breeding research.