This project contains proteomic profiles of shell matrix proteins (SMPs) from the Iwagaki oyster Crassostrea nippona, covering both life stage-specific shells (D-stage larval and adult shell) and shell microstructure-specific layers (prismatic, foliated, and chalky layers of the adult shell). These datasets were generated to investigate the molecular composition and regulatory mechanisms underlying biomineralized shell formation across developmental stages and shell architectures. The identified proteins provide insights into shell mineralization from both structural and evolutionary perspectives.