With the continuous progress of technology, computed tomography (CT) technology has expanded from medicine to agriculture and other industries. With the advantages of non-destructiveness, high resolution, and high precision, CT technology shows great application potential in the agricultural field. However, there are still some problems with this technology that need to be solved. This paper aims to show the application of CT technology in the agricultural field, find technical challenges, and put forward specific countermeasures, so that CT technology can be better applied in the agricultural field. This paper summarizes the application of CT technology in the quality detection of agricultural products, disease and insect pest identification, seed screening, soil analysis, and precision agriculture management, and focuses on the current challenges and the countermeasures, and looks into the role of this technology in promoting agricultural development in the future. Despite various challenges, CT technology has far more advantages than disadvantages, and it is expected to become an indispensable part of all the links of agricultural production and promote the development of precision agriculture and smart agriculture.