Abstract: Crop seeds are small, with rich internal and external details of morphology. Traditional methods were difficult to obtain high-resolution morphological data and accurately calculate phenotypic parameters. In this paper, the three-dimensional（3 D） data of maize, rice, and cotton seeds were obtained using high-resolution 3 D scanner and micro CT. Surface area and volume for phenotypic penameters of the seeds were calculated using the acquired data. Advantages and disadvantages of the two methods were compared and analyzed with respect to cost, automation, and efficiency of acquisition process. Results showed that 3 D digitization of crop seeds required the resolution of the data acquisition equipment had less than than 20 μm. The two methods introduced both could achieve high-resolution 3 D data acquisition and phenotypic parameter calculation of crop seeds. The calculation results could reflect the differences among species, cultivars, and individual seeds. The external data with color information could be obtained by 3 D scanning of the outlier surface, and the high-quality data inside and outside the seed could be obtained by micro CT. The two 3 D digitization methods were expected to provide technical support for high-resolution morphological data acquisition, phenotypic parameter calculation, and quality detection for crop seeds.