In order to obtain the genetic basis of transcriptome data of Orychophragmus violaceus seedlings, the transcriptome of Orychophragmus violaceus was paired-end sequenced by Illumina Novaseq 6000 platform, a total of 59174171 clean reads (17.75 Gb clean bases) were obtained, and 110919 unigenes were obtained after assembly by de novo, with the longest and shortest length of 15030, 301 bp and an average length of 784 bp. The N50 was 947 bp and the N90 was 396 bp. These unigenes were compared among seven public databases including Non-redundant protein sequences (NR), Nucleotide (NT), Swiss-prot protein database (Swiss-Prot), Protein family (Pfam), Eu-karyotic ortholog groups (KOG), Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG), as a result of 75369 (67.94%), 69004 (62.21%), 62258 (56.12%), 56068 (50.54%), 27796 (25.05%), 56066 (50.54%), 32897 (29.65%) unigenes were annotated respectively. These annotation results showed that Orychophragmus violaceus had most homologous sequences with 13610 unigenes with Quercus suber. The GO annotations showed that 56066 unigenes were annotated with 219038, which were divided into 3 categories and 43 functional groups. The KOG annotations showed that 27796 unigenes were annotated and grouped into 25 functional categories. The KEGG annotations showed that 32897 unigenes were involved in 34 types of metabolic pathways and 305 metabolic pathway branches. A total of 18118 SSR sites and 112584 CDS sequences were detected according to analyzing the coding sequences and microsatellite. Base on the high-throughput transcriptome sequencing of Orychophragmus violaceus, with a large number of functional genes are excavated, which provide certain basic data support for the subsequent development of bioinformatics analysis such as molecular markers and functional metabolic pathways.