Mantle is a mollusk organ at the forefront of the biomineralization process. FESEM was used to study the microstructure of the gastropod shell, as well as histological methods, histochemical methods, and transcriptome processing on the mantle and foot, to understand how different mantle regions play different roles in cross-laminated structure. Chicoreus torrefactus, which has a characteristic cross-lamellar structure, was utilized as a ideal species in our study to investigate the structure and function of the mantle in shell formation. After the data was assembled and de-redundant, the transcriptomes of three sections of the mantle edge, mantle central, and foot were sequenced, yielding a total of 110,156 unigenes. Morphological differences detected by histology of the two mantle regions were linked to functional heterogeneity by selecting the top five most abundant Pfam domains in the annotated 2002 differentially abundant transcripts across the mantle central, mantle edge, and foot. Calcium ion binding was detected in both the mantle edge and the mantle central. The mantle edge is rich in chitin binding of GO functions linked with biological scaffolding. The EF-hand domain linked with calcium ion signal regulation is highly enriched in the mantle central. Our results provide a preliminary basis for studying the formation mechanism of cross-lamellar shell structures.