The rapid, efficient and non-destructive 3D morphological data acquisition of plants are great significance to the study of digital plant, functional structural plant model and crop phenotype. This paper discusses 3D data acquisition methods for smaller plant organs, which take maize grain as an example. Smartscan and Micro-CT scanning can be used to obtain the morphological data of the grains. The efficiency, accuracy, processing of data in two scanning ways are compared and analyzed. The results shows that the Micro-CT is more suitable for obtaining information of internal structure of maize grain. While grain morphology in SmartScan can get better visualization than Micro-CT, and the former one can also obtain image texture information. These two kinds of methods for volume measurement have good consistency except for Denghai 605. The study will provide theoretical basis for obtaining 3D data of plant organs at smaller scales.