Galactooligosaccharides are composed mainly of galactosyl lactose, which is important for infant growth and as a functional food additive. Although galactosyl lactose is abundant in goat milk, its complex structure has hindered the separation and analysis of its isomers. In this study, 5 isomers of goat milk galactosyl lactose were separated by HPLC: β6′-galactosyl lactose (β6′-GL), α6′-galactosyl lactose (α6′-GL), β4′-galactosyl lactose (β4′-GL), α3′-galactosyl lactose (α3′-GL), and β3′-galactosyl lactose (β3′-GL). This composition differs from that of commercial galactooligosaccharide products, which comprise mainly β-configuration oligosaccharides. The isomers were then qualitatively and quantitatively compared at different lactation stages using online HPLC-mass spectrometry. Relative quantitative analysis showed that the total content of the 5 galactosyl lactose isomers was highest in transitional goat milk. Specifically, β3′-GL was the main isomer in colostrum and α3′-GL was the main isomer in transitional and mature milk. β6′-Galactosyl lactose and β4′-GL tended to increase and then decrease during lactation. Moreover, α3′-GL content was 2 times higher than in colostrum and 10 times higher in transitional milk than in mature milk; in contrast, for β3′-GL, the values were 5 and 2 times higher, respectively. Absolute quantitative analysis revealed that β3′-GL was the most abundant isomers in colostrum (32.3 mg/L), and α3′-GL was the most abundant in transitional milk (88.1 mg/L) and mature milk (36.3 mg/L). These findings provide an important quantitative basis for understanding the relationship between structure and function of galactosyl lactose in goat milk, as well as its exploitation as a functional food.