Plants have efficient water-transporting vascular networks with a self-recovery function from embolism, which causes fatal discontinuity in sap flow. However, the embolism-refilling process in xylem vessel is still unclear. The water-refilling processes in the individual xylem vessels of excised Arabidopsis roots were visualized in this study using synchrotron X-ray micro-imaging technique with high spatial resolution up to 1 μm per pixel and temporal resolution up to 24 fps. In normal continuous water-refilling process, we could observe various flow patterns affected by the morphological structures of the xylem vessels, especially when water passed through perforation plates. A simple criterion based on the variation in dynamic pressure was suggested to evaluate the contribution of individual perforation plates to the water-refilling process. Meanwhile, the water-refilling embolized sections of xylem vessels through radial pathways were also observed. Separated water columns were formed from this discontinuous water-refilling process and the water influx rates through the radial pathways were estimated to be 478 and 928 μm(3) s(-1). The dynamic behavior of the separated water columns were quantitatively analyzed from the stoppage of volume growth to the translational phase. These water-refilling processes in excised roots of Arabidopsis may shed light on understanding the water refilling in the embolism vessels of intact plants and the interconnectivity of xylem vessel networks in vascular plants.