Otoliths serve as elegant models for biologically controlled biomineralization, utilizing similar macromolecular machinery to achieve distinct polymorph selection. Here, we demonstrate how the intrinsically disordered protein Starmaker (Stm) utilizes conformational flexibility and post-translational modification to direct calcium carbonate phase selection. Stm adopts an expanded conformation with high Ca²⁺ capacity, and its compaction is finely tuned by monovalent ions. In the presence of Ca²⁺ and Mg²⁺, Stm undergoes liquid–liquid phase separation (LLPS), generating a fluid amorphous precursor that yields aragonite over calcite. Beyond ionic modulation, we show that native phosphorylation patterns act as an essential molecular switch for polymorph selection: Stm isolated from vaterite otoliths directs vaterite formation in vitro, whereas identical protein sequences with artificial phosphorylation or dephosphorylation yield calcite. These findings provide the first direct demonstration that a single isolated protein switches calcium carbonate polymorphs based on its phosphorylation pattern, revealing how ionic cooperative tuning and post-translational modifications govern non-classical biomineralization pathways.