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The SRY-type HMG box 9 (<i>Sox9</i>) gene plays an important role in chondrocyte development as well as changes in hypertrophic chondrocytes, indicating that <i>Sox9</i> can regulate growth in animals. However, no studies to date have examined the correlation between variations in <i>Sox9</i> and growth traits in goats. Here, we found a 4 bp indel in the 3′UTR of <i>Sox9</i> and verified its association with growth traits in Shaanbei white cashmere goats (<i>n</i> = 1109). The frequencies of two genotypes (ID and II) were 0.397 and 0.603, respectively, and polymorphic information content (PIC) values showed that the indel had a medium PIC (PIC > 0.25). The 4 bp indel was significantly correlated with body length (<i>p</i> = 0.006), heart girth (<i>p</i> = 0.001), and hip width (<i>p</i> = 4.37 × 10 ⁻⁴). Notably, individuals with the ID genotype had significantly superior phenotypic traits compared with individuals bearing the II genotype. Hence, we speculated that the 4 bp indel is an important mutation affecting growth traits in goat, and may serve as an effective DNA molecular marker for marker-assisted selection in goat breeding programs.