Alaska pollock proteins (PPs) are aquatic proteins with a compact structure, which leads to poor solubility and limited application in food industries. This study explored the structural assembly and gelation behavior of the PP-soluble aggregates prepared by the refolding processing of acidic (pH 1.5-7) or alkaline (pH 12-7) pH-shifting treatment. PPs refolded at alkali pHs produced more soluble aggregates than at acid pHs. Lots of myosin heavy lights (MHCs) could interact with actin to form soluble aggregates at high pH rather than low pH. When shifting back to pH 7, the solubility of alkaline-shifted PPs was boosted to over 60% with a more flexible structure, while acidic-shifted PPs showed reduced solubility (29%) with increased rigidity. Molecular characteristics results indicated that alkaline-shifted PPs comprising MHCs and actin exhibited higher surface hydrophobicity and sulfhydryl groups. These structural modifications induced by alkaline pH-shifting contributed to improving the gelling, emulsifying and foaming properties of PPs. Intriguingly, both acidic- and alkaline-shifted PPs showed a retarded digestive behavior. These novel insights may be adaptable to other animal proteins for modulating the protein structure-functionality, expanding their applications in food industries.