The localizations of sodium exclusion are roots and stem base, however, Na + distribution in these localizations is unclear.Here, we used a salt-tolerant buckwheat cultivar Chuanqiao No.1 and a salt-sensitive cultivar TQ-0808 to demonstrate Na + distribution. We found that Na + content was highest in vacuole, the following was in cell wall or free space, and the least was in cytoplasm. Comparative analysis shows that Na + accumulation in vacuole, cell wall, or free space of roots and stem base in 'Chuanqiao No.1' was obviously higher than in 'TQ-0808'; in contrast, Na + accumulation in cytoplasm of 'Chuanqiao No.1' was less than in 'TQ-0808'. These results indicate that the capabilities of Na + extrusion and Na + compartmentalization of salt-tolerant buckwheat were obviously higher than of the salt-sensitive one, and the capabilities could effectively restrict Na + transport to shoot. Compartmentalization of Na + in the vacuole was the main way for Na + exclusion of salt-tolerant buckwheat. In addition, the transcriptions of Na + /H + antiporter 1 and salt overly sensitive 1 were remarkably higher in 'Chuanqiao No.1' than in 'TQ-0808', which is consistent with the above results.