Eucommia ulmoides Oliv contains many kinds of active and nutritional components, which have important medicinal and nutritional value. In order to reveal the cultivation technology of Eucommia ulmoides and molecular regulation mechanism of axillary bud development, illumina hiseq high-throughput sequencing technology was used to extract mRNA from the top and basal dormant buds, and axillary buds of the plant after stubble, then the transcriptome sequencing analysis was conducted. The results showed that 29353 UniGenes were annotated, and the annotation rate was 30.04%, the remaining 68367 UniGenes were not annotated, which may be new genes; The number of genes differentially expressed (DEGs) in Eucommia ulmoides axillary bud was the highest after stubble treatment, a total of 5384 genes were detected, which 3137 genes were up-regulated and 2247 genes were down regulated. The number of differentially expressed genes was the least in the top and basal dormant buds. The functional analysis of COG, GO and KEGG genes showed that axillary bud differential genes were enriched in the biological processes and metabolic pathways related to primary metabolism, secondary metabolism, and plant hormone signal transduction pathway. The key genes of flavonoid and phenylpropane synthesis and the expression level of abscisic acid (ABA) regulating the dormancy of axillary buds were down-regulated, which promoted the release of the dormancy of axillary buds. At the same time, auxin response genes such as AUX / IAA, GH3, ARF and SAUR and primary cytokinin response genes such as AHP and A-ARR were up-regulated, which promoted the synthesis of auxin and cytokinin in axillary buds, marking the beginning of axillary bud development. The gene expression patterns of the two dormant buds were consistent, mainly concentrated in photosynthesis related pathways. Real time PCR showed that the expression profile of DEGs was consistent with that of RNA sequencing. This study provides basic data for the cultivation and molecular breeding of Eucommia ulmoides.