To understand the role of long noncoding RNA (lncRNA) gene regulation and changes in expression in mouse external ear embryonic development, a BMP5 short ear mouse model was used to measure changes in the lncRNA expression in the outer ear tissues of mouse embryos developed to E15. 5 and E17. 5 using high-throughput sequencing. The changes in lncRNA expression were identified using find_circ and CIRI2 software, and functional analyses were performed using gene ontology and the Kyoto encyclopedia of genes and genomes annotations of differentially expressed lncRNAs. The results show a correlation between the regulation of lncRNA and some key regulatory lncRNA changes after point mutations in BMP5. This study provides new insights into the mechanism, by which lncRNAs regulate the development of the mouse's external ear. The change in lncRNA expression profiles can also provide clues for the study of the regulatory mechanisms of external ear embryonic development.