Insight into the architecture and the interaction between components in fully mature rice are difficult to study but are important to its processing technology and quality control as it is mainly consumed as the whole kernel. In this study, different microscopy techniques were combined to explain the differences of rheological and thermal properties between rice kernel and its flour even though they had the same compositions. The area and positions of the endothermic peaks of starch, flour, and kernel were different. The uneven distribution of starch granules and part of the protein bodies were observed by a scanning electron microscope. The regional distribution and spatial structure of starch granules and cell walls showed the restriction effect of kernel structure of rice. The clear fluorescence by a confocal laser scanning microscope showed that the protein bodies and cell walls formed barriers in rice to delay the hydration and limit the expansion of starches. Overall, the structural form of rice is closely related to its physicochemical properties.