BCL11B is a transcription factor, which contains profound effects on the aorta, contractile properties of resistance vessels, and blood pressure. However, the mechanism of how BCL11B regulates the aorta function is not fully understood. In this study, our study is to identify the key molecules and signaling pathways by analyzing the RNA-seq data. The GSE163551 was produced by the Illumina NextSeq 500 (Mus musculus). The KEGG and GO analyses showed the ribosome and calcium signaling pathways are the main processes during the BCL11B knockout. Moreover, we determined ten key molecules including RPS11, GATA4, RPS13, RPL9, RPL27A, RPS24, RPL23A, RPL37A, BMP4, RPS7. Thus, our study may provide novel knowledge of the BCL11B regulated aorta.