Abstract: Micro computed tomography (micro-CT) has become a crucial research tool in the medical and biological fields, but it is just starting to be applied in the area of plant, agriculture and forestry science. In order to enable micro-CT method more fully and flexibly application in the area of plant, agriculture and forestry science, as well as improve the application performance and develop the potential demands of the instrument, this article introduces the fundamental principle, sample preparation and analysis procedures during micro-CT application. Finally, by using the rice grain as an example, cross-section image analysis, 3D reconstruction and structure analysis of rice grain were carried out in Mimics software. This paper can provide a reference for researchers to analyze plant samples by using micro-CT technology, so as to better serve the teaching and scientific research work.