Native whey protein and casein micelles in goat milk often struggle to exhibit desirable functional properties, such as poor heat stability of whey protein and low solubility of casein. To address these limitations, this study applied ultrasound treatment to goat milk and heat-sterilized goat milk to improve protein functionalities, including solubility, foaming, emulsification, and digestibility. The results showed that the optimal treatments to improve the functional properties of goat milk protein were 400W, 7 min. Under these conditions, whey protein and casein surface hydrophobicity increased to 167,578.90 and 444,658.87 +/- 2745.48 (P < 0.05). Meanwhile, the results of circular dichroism, fluorescence spectrum and SDS-PAGE revealed that ultrasound treatment weakened the hydrogen bonding and hydrophobic interaction within the components of protein, resulting in protein structure unfolding and increased flexibility. These changes increased the solubility of casein and optimized the foaming, digestibility and emulsification properties of goat milk protein. Additionally, ultrasonic treatment effectively disperses heat-aggregated goat milk proteins, reducing the particle sizes of whey protein from 3370 nm to 1434.67 nm and casein from 796.5 nm to 355.95 nm. This treatment not only enhances the functional properties of the proteins but also extends the storage stability of pasteurized goat milk to 12 days.