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Copy number variations (CNVs) have many forms of variation structure, and they play an important role in the research of variety diversity, biological evolution and disease correlation. Since CNVs have a greater impact on gene regulation and expression, more studies are being finalized on CNVs in important livestock and poultry species. The <i>protein phosphatase 3 catalytic subunit alpha</i> (<i>PPP3CA</i>) is a key candidate gene involved in the goat fecundity trait, and has important effects on precocious puberty, estrogen signal transduction pathways and oocyte meiosis. Additionally, <i>PPP3CA</i> also has a dephosphorylation effect in the process of spermatogonial stem cell meiosis and spermatogenesis. So far, there is no research on the relationship between the copy number variations of the <i>PPP3CA</i> gene and reproduction traits. Therefore, the purpose of this study was to determine the association between copy number variations in the goat <i>PPP3CA</i> gene and litter size and semen quality in Shaanbei white cashmere goats (SBWC) (<i>n</i> = 353) and Guizhou Heima goats (<i>n</i> = 64). Based on the association analysis, the results showed that only CNV1 and CNV2 within the <i>PPP3CA</i> gene were distinctly related to the first-birth litter size in female goats (<i>p</i> = 7.6802 × 10⁻¹¹; <i>p</i> = 5.0895 × 10⁻⁹, respectively) and they were also significantly associated with the semen quality of SBWC goats (<i>p</i> < 0.05). In addition, individuals with Loss genotypes demonstrated better phenotypic performance compared to those with other types. Therefore, CNV1 and CNV2 of the <i>PPP3CA</i> gene are potentially useful for breeding, as they are linked to important goat reproduction traits.