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<i>Janus kinase 2</i> (<i>JAK2</i>) plays a critical role in myoblast proliferation and fat deposition in animals. Our previous RNA-Seq analyses identified a close association between the <i>JAK2</i> gene and muscle development. To date, research delving into the relationship between the <i>JAK2</i> gene and growth traits has been sparse. In this study, we sought to investigate the relationship between novel mutations within the <i>JAK2</i> gene and goat growth traits. Herein, two novel InDel (Insertion/Deletion) polymorphisms within the <i>JAK2</i> gene were detected in 548 goats, and only two genotypes were designated as ID (Insertion/Deletion) and DD (Deletion/Deletion). The results indicate that the two InDels, the del19008 locus in intron 2 and del72416 InDel in intron 6, showed significant associations with growth traits (<i>p</i> < 0.05). Compared to Nubian and Jianzhou Daer goats, the del72416 locus displayed a more pronounced effect in the Fuqing breed group. In the Nubian breed (NB) group, both InDels showed a marked influence on body height (BH). There were strong linkages observed for these two InDels between the Fuqing (FQ) and Jianzhou (JZ) populations. The DD-ID diplotype was associated with inferior growth traits in chest width (ChW) and cannon circumference (CaC) in the FQ goats compared to the other diplotypes. In the NB population, the DD-DD diplotype exhibited a marked negative impact on BH and HuWI (hucklebone width index), in contrast to the other diplotypes. In summary, our findings suggest that the two InDel polymorphisms within the <i>JAK2</i> gene could serve as valuable molecular markers for enhancing goat growth traits in breeding programs.