ABSTRACT As a key representative of marine traditional Chinese medicine, Margaritifera Concha is commonly processed by calcination. However, significant differences in processing methods and quality standards have led to considerable variations in the quality of decoction pieces. Based on the theory of “quality evaluation through morphological identification,” this study investigates the microstructure and crystal phase composition of Margaritifera Concha and its calcined products, aiming to establish a new quality control approach distinct from traditional chemical index‐based models. The microstructure of the “brick wall‐cement‐brick wall” pattern in Margaritifera Concha was examined using scanning electron microscopy and microscopic computed tomography, followed by 3D reconstruction and porosity calculations. The crystal phase composition was analyzed using x‐ray diffraction, thermogravimetric analysis, and Fourier transform infrared spectroscopy. The results indicate that the calcination of Margaritifera Concha is closely associated with changes in its microstructural characteristics, and porosity can serve as a quantitative index for assessing the processing degree of decoction pieces.