Numerous studies have highlighted the role of X-ray computed tomography (X-ray CT) in understanding root architecture. Nevertheless, setting definitive scanning parameters for diverse soils in varied container sizes remains challenging. This study investigates the influence of X-ray CT system voltage on the penetration capability in diverse soils and container sizes, focusing on two key parameters: (1) gray values, which indicate X-ray attenuation and contribute to image contrast, and (2) signal-to-noise ratio, a measure of image clarity. Five soil samples were collected from various depths within a soil profile to encompass bulk density values ranging from 1.34 to 1.84 g·cm−3 to conduct the experiment. Containers with dimensions of 6 × 6 × 6 cm³, 8 × 8 × 6 cm³, 10 × 10 × 6 cm³, 12 × 12 × 6 cm³, 14 × 14 × 6 cm³, and 16 × 16 × 6 cm³ were used. Voltage levels spanning 75 to 225 kV, in 25-kV increments, were applied to each sample. The observed gray values of the X-ray images were fitted using a logistic model of three parameters. Results showed that increasing voltage leads to enhanced penetration up to a plateau point, irrespective of soil density or container size. This plateau could potentially yield higher quality scans, given that lower voltages result in subdued gray values and reduced image contrast. Notably, it was observed that soil properties, including mineral composition, directly affect image gray values. This study established optimal voltage settings for specific soil types at fixed densities, offering valuable insights for researchers investigating soil–root interactions. Although the current findings are based on five soils, a more extensive sampling encompassing diverse soil textures and densities is necessary for a comprehensive understanding of X-ray penetration behavior across various soil types.