Smart microstructure design of dosage forms such as microcapsules that protect the microorganism, can improve probiotics survival from gastric pH challenges and prolong their shelf life. In this study, synchrotron radiation X-ray microcomputed tomography (SR-μCT) was applied to quantitatively reveal the material distributions and functional structures of bifidobacterium and lactobacillus microcapsules. The shell layer, middle protective layer, and the microorganisms as particles in the center layer were extracted and visualized. All the microorganisms were encapsulated by the shell completely, which prevents them from being destroyed by external environments. However, the non-uniform thickness of the shell and typical defects in the microcapsules were observed. The quantitative analysis and characterization of internal microstructures provide evidence of the need for further improvement in formulations and processing technologies for the structured system to deliver living microorganisms.