S100A7 is an inflammation-related protein and plays an essential role in host defenses, yet there is little research about the relationship between mastitis and S100A7 expression in dairy goats. Here, according to the clinical diagnosis of udders, SCC, and bacteriological culture (BC) of milk, 84 dairy goats were grouped into healthy goats (n = 25), subclinical mastitis goats (n = 36), and clinical mastitis goats (n = 23). The S100A7 concentration in subclinical mastitis goats was significantly upregulated than in healthy dairy goats (p = 0.0056) and had a limited change with clinical mastitis dairy goats (p = 0.8222). The relationship between log10 SCC and S100A7 concentration in milk was positive and R = 0.05249; the regression equation was Y = 0.1446 × X + 12.54. According to the three groups, the log10 SCC and S100A7 were analyzed using the receiver operating characteristics (ROC) curve; in subclinical mastitis goats, the area under the ROC curve (AUC) of log10 SCC was 0.9222 and p < 0.0001, and the AUC of S100A7 concentration was 0.7317 and p = 0.0022, respectively; in clinical mastitis goats, the AUC of log10 SCC was 0.9678 and p < 0.0001, and the AUC of S100A7 concentration was 0.5487 and p = 0.5634, respectively. In healthy goats, S100A7 was expressed weakly in the alveolus of the mammary gland of healthy goats while expressed densely in the collapsed alveolus of mastitis goats. Moreover, S100A7 expression increased significantly in mastitis goats than in healthy dairy goats. In this research, results showed the effects of mastitis on the S100A7 expression in the mammary gland and S100A7 concentration in milk and the limited relationship between SCC and mastitis, which provided a new insight into S100A7’s role in the host defenses of dairy goats.