Two whey protein isolate amyloid fibrils (WPIF) with different structure were prepared, and the effects of these structures on binding of β-carotene (BC) and in vitro digestibility were evaluated. Whey protein isolate (WPI) in water (80 °C, pH 2.0) self-assembled into elongated WPIF (E-WPIF), whereas WPI formed to worm-like WPIF (W-WPIF) in trifluoroethanol. Compared to E-WPIF, W-WPIF showed higher surface hydrophobicity, indicating exposure of more hydrophobic residues. The encapsulation efficiency and loading capacity of BC in W-WPIF were higher than that of E-WPIF. The hydrophobic interaction were the main driving forces of WPIF/BC. During gastric digestion, WPIF lost intact fibrils structures, resulting in unordered small aggregates and most BC still bound to them. Then they were destroyed in the following intestinal digestion, leading to the release of BC. Compared with W-WPIF/BC, E-WPIF/BC had higher release of BC in gastrointestinal digestion due to weaker binding of BC and better digestibility of E-WPIF.