Research on the shells microstructures of thirteen species of bivalve which belong to six family using the scanning electron microscope (SEM). The 13 species are respectively Meretrix lusoria，Meretrix lyrata，Meretrix meretrix，Paphia undulata，Ruditapes philippinarum，Ruditapes variegata，Clausinella isobellina，Anadara clathrata，Tegillarca granosa，Chlamys farreri，Sanguinolaria aauta，Coecella turgida，Atrina pectinata. Methods: Three samples from each structure were fixed with 2.5% pentanediol, and then, cut the shells separately into 0.5 cm x 0.5 cm of small pieces. All sections of small pieces should be grinded before observed by the scanning electron microscope. Samples would be measured and taken pictures after them were observed. Resluts:The results show that the shell surface microstructures have some differences in different species. These differences mostly manifested in the compose and arrangement of the crystal. There are five types in the shell surface morphology of the corneum：smooth，granular，irregular polygon and special honeycomb structure. The crystal of the shell prismatic layer are prism-like shapes,short column,flakes and irregular shape. There are two kinds of directions in the arrangement of the crystals in different shells: perpendicular to the cross-section，another is parallel to the cross-section．The shape of the crystal in nacre of thirteen kinds of shells are granular,brick-shaped,rounded shape,massive and irregular polygons.The thickness of the corneum,prismatic layer and nacre in different shells are also different．Conclusion:Research on the microstructure of the shells，so that to provide a basis for classification.