The Gigantidas haimaensis, a key species in the extreme environment of Haima cold seep of the South China Sea, relies on its shell for protection. Shell matrix proteins (SMPs) are crucial for shell formation. Prior research mainly focused on shallow-sea mollusks but less on deep-sea clam. In this study, we observed that the microstructure of G. haimaensis shells consisted of a single block of aragonite, which formed six pearl aragonite lamellae and the nacre. Proteomics identified 231 SMPs, two conserved SMPs (SMP1 and Pif-like) were found. We have characterized an extremely acidic protein Gh26, and obtained its recombinant protein by expression and purification. Quantitative real-time PCR (qPCR) shows that Gh26 has the highest expression level in the mantle. Gh26 can simultaneously bind calcite and aragonite but negatively regulates their crystallization, inhibiting their crystallization rate. In the aragonite crystallization system, high concentrations of Gh26 can induce calcite nucleation and inhibit aragonite nucleation. This demonstrates the versatility of Gh26 in regulating calcite crystal morphology. The multifunctionality of Gh26 enhances the adaptability of G. haimaensis's biomineralization function in the deep-sea environment, which is important for a deeper understanding of SMP composition and characteristics in deep-sea clams and the adaptations of deep-sea mollusks' SMPs.