Protein properties can be modified by thermal treatment at different pH values, resulting in the formation of protein aggregates with diverse morphologies and functionalities. This study investigated the morphology of aggregates of Antarctic krill protein (AKPS) formed by thermal treatment (90 °C, 15 min) at pH 2, 3, 4, and 6−12, characterized the different morphologies of AKPS, and determined the metal ion (Ca 2+ , Fe 2+ , and Zn 2+ )-binding capacities. Results showed that heat treatment with different pH values generated various AKPS with distinct morphology and metal ion-binding abilities. AKPS have formed fibrils at pH ≤ 3, particles at pH 4−7, and amorphous aggregates at pH ≥ 8. Fibrous AKPS (pH 2) exhibited a high solubility (80.36%) and strong reducing effect on iron. The binding capacities of Ca 2+ and Fe 2+ reached 36.08% and 66.75%. Particulate AKPS (pH 6 and 7) primarily only showed Zn 2+ -binding capacity similar to that of casein phosphopeptide (17.33%). Amorphous AKPS (pH 9−11) displayed the optimal capacity to bind Zn 2+ and Fe 2+ (26.90% and 74.94%). The alterations in morphology and functional characteristics of AKPS permit the design of various nanostructures for food-derived mineral supplements, thus developing their potential for application in functional foods.