Objective Compared with the wild type mice, the homozygous ETV5 knockout mice prepared by CRISPR/Cas9 technology showed significant weakness in body size and body weight along with endogenous spermatogonial stem cell ablation. The purpose of this study was to explore the effect of ETV5 knockout on the muscle expression profile of mice.Method The muscle tissues of three wild-type male mice and three ETV5 homozygous knockout male mice aged six weeks were collected and total RNA was extracted for transcriptome sequencing. We analyzed the sequencing results using bioinformatic method. Cluster analysis, GO and KEGG enrichment analyses were performed on the differentially expressed genes in the muscle samples of two groups of mice.Result A total of 574 differentially expressed genes were screened out from the muscle tissues of two groups, including 292 up-regulated genes and 282 down-regulated genes. Several genes were found to affect the growth and development of ETV5 knockout mice. These genes included Amd1 affecting muscle development of mice, and Chrna2 affecting fat accumulation. Most of the pathways enriched by GO and KEGG analyses were related to fat metabolism and growth and development.Conclusion These results provide an explanation for the molecular mechanism of abnormal development of ETV5 knockout mice, and provide references for further study of in vivo function of ETV5 gene.