α-Lactalbumin (α-LA), the primary whey protein in human milk, is rich in essential amino acids and plays a crucial role in infant growth and development. This study investigated the effects of different calcium (Ca) binding levels on the structural characteristics and gastrointestinal digestive behavior of bovine, goat and human α-LA. We used spectroscopic techniques to detect changes in the secondary and tertiary structure of α-LA and analyzed thermal stability with differential scanning calorimetry. Decalcification led to partial unfolding of α-LA, resulting in a more open conformation and significantly reduced thermal stability. Additionally, decalcification increased the in vitro digestibility of α-LA under the infant digestion condition, diminishing its resistance to pepsin and yielding more small peptides and free amino acids. Conversely, higher Ca content slightly affected the structure of α-LA and reduced its digestibility. Bovine, goat and human α-LA exhibited differences in structure and digestion patterns. Human α-LA showed the lowest gastric digestibility, with hydrolysis occurring mainly on large peptides rather than intact proteins. However, during intestinal digestion, human α-LA demonstrated higher digestibility than bovine and goat α-LA, releasing more small peptides and amino acids for more complete digestion. These results provide insights into the relationship between the structure and digestibility of α-LA, which can inform the formulation of infant formulas aimed at optimizing protein digestion and nutrient absorption.