One of the most precise methods of tracking water movement and measuring moisture content during hydration process is the usage of magnetic resonance imaging (MRI). In this study, the target samples were dried “Robusta” green coffee beans, and a series of images was acquired through an MRI system during the entire hydration process. Coffee beans were immersed in a glass bottle and were placed in a 35 mm diameter RF coil throughout the whole experiment. A set of 64 images with a field of view of 26 mm×26 mm was acquired. The hydration process of intact dried green coffee beans lasted for 360 min and image data sets were acquired every 10 min with an optimal GRE pulse sequence developed. The MR images were analyzed in 2D and 3D imaging spaces. The results of 2D analysis showed that the changes in water penetration depth inside coffee beans during the hydration process could be visualized. In addition, the results of 3D analysis presented a clearer understanding of the hydration process of dried coffee beans. This study showed that changes in water distribution and physical dimensions of coffee beans during the hydration process in 2D and 3D imaging spaces were meserable, without disturbing the process, by means of the MRI technique.