The fingerprints of goat milk and infant goat milk formulas were established based on near-infrared spectroscopy (NIRS). In addition, the fingerprint-based principal component analysis (PCA) was used to identify infant goat milk formulas at different stages, whether goat milk was mixed with bovine milk, and whether goat milk formulas were mixed with desalted bovine whey powder. The results showed that there were six and nine characteristics of common maximum absorption intensity in goat milk and infant goat milk formulas, respectively. Among them, the NIR wavenumbers corresponding to the characteristic maximum absorption intensity of goat milk are: 10270.95, 8612.31, 8334.77, 6914.12, 5539.54, and 5202.52cm− 1, and the NIR wavenumbers corresponding to the characteristic maximum absorption intensity of infant goat milk formulas are: 8262.08, 6795.08, 6352.36, 5790.64, 5684.91, 5162.87, 4753.17, 4368.86, 4257.56 cm− 1. The method of combining NIRS and PCA was used to identify Stage 1, 2, and 3 of infant goat milk formulas. The use of the method combining NIRS and PCA enabled the discrimination of Stage 1, 2, and 3 of infant goat milk formulas. It was able to effectively identify adulterated desalted bovine whey powder from desalted goat whey powder and adulterated bovine milk from goat milk. The results suggested that different stages of infant goat milk formulas and goat milk and its infant formulas adulteration could be differentiated by NIRS combined with PCA, which provided convincing evidence for the identification and brand protection of goat milk and infant goat milk formulas.