Collagen is an important biopolymer widely used in food, cosmetics and biomedical applications. Understanding the effect of pH on the structure and properties of collagen is beneficial for its further processing and exploitation. In this study, greenfin horse-faced filefish skin collagen (GHSC) was prepared and identified as a type I collagen. We systematically investigated the effect of pH on the structural, functional and rheological properties of GHSC. Scanning electron microscopy showed that the collagen morphology changed from an ordered stacked sheet structure to a rough silk-like structure as pH increased. Gaussian-fitted Fourier infrared spectroscopy results of the collagen revealed that it unfolded with increasing pH. Moreover, the ordered structure was reduced, and random coils became the dominant conformation. Its β-sheet and random coil contents increased from 18.43 ± 0.08 and 33.62 ± 0.17 to 19.72 ± 0.02 and 39.53 ± 1.03%, respectively, with increasing pH. α-helices and β-turns decreased from 35.00 ± 0.26 and 12.95 ± 0.01 to 29.39 ± 0.92 and 11.36 ± 0.10%, respectively. The increase in β-sheets and random coils allowed the pI-treated collagen to exhibit maximum water contact angle. The emulsification and foaming properties decreased and then increased with increasing pH in a V-shape. The increased net surface charge and β-sheets in collagen benefited its emulsification and foaming properties. The rheological results showed that the protoprotein exhibited shear-thinning properties in all pH ranges. The collagen solutions showed liquid-like behaviour in low-pH (2, 4) solutions and solid-like behaviour in high-pH (6, 7.83 and 10) solutions. Moreover, the frequency-dependent properties of the storage modulus (G') and loss modulus (G″) of the collagen solutions weakened with increasing pH. Collagen has considerable frequency-dependent properties of G' and G″ at low pH (2, 4). Thus, the importance of collagen raw material preparation for subsequent processing was emphasised, which may provide new insights into applying collagen-based materials in food, biomaterials and tissue engineering.