Based on the processing by IBM SPSS software, SOX6-CNV was significantly correlated with the chest girth of the 6-months old yaks ( p < 0.05) and 30-months yaks ( p < 0.05), and withers height of 6 months yaks ( p < 0.05) and 18-months yaks ( p < 0.05), as well as the normal type of CNV, was chosen for yak breeding. The experiment results demonstrated the expression of SOX6 in each tissue, and the kidney and muscle tissue were found to have higher relative expression levels. Furthermore, the SOX6 gene expression was identified in seven different tissues of the yaks. This study employed quantitative real-time fluorescence quota PCR (qPCR) for detecting the SOX6-CNV of the 311 Ashidan yaks and analyzed the correlation of the SOX6-CNV with four phenotypes (including body weight, withers height, body length, and chest girth) of the yaks aged 6, 12, 18, and 30 months using ANOVA and multiple comparisons. The SOX6 gene (sex-determining region Y-box 6), as a transcription factor, has multiple functions with regard to sex determination, embryonic growth, the nervous system development, as well as bone, and various organ formation. Copy number variation (CNV) is a fundamental type of structural variation of the genome affecting the economic traits of livestock.