After Minamata disease occurred in Kumamoto Prefecture, the Minamata Bay Pollution Prevention Project on Minamata Bay area was started to deal with mercury pollution. Beneficial from the project, the mercury content in the bay area has been significantly reduced. However, many studies have shown that the residual trace mercury content around the bay is still high. Furthermore, mercury has migrated from Minamata Bay to the Yatsushiro Sea. Therefore, continuous research on the distribution and content of mercury in this region is required.In this study, using sediment classification, the relationship between sediment particle size, particle specific surface area, and T-Hg (total mercury) concentration was investigated. Based on the numerical simulation, the particle size effect on the migration of mercury-containing sediments and the T-Hg distribution in the Yatsushiro Sea were studied. The result showed that the larger the particle size, the lower the T-Hg concentration in the sediment. Meanwhile, the larger the particle specific surface area, the higher the T-Hg concentration. Moreover, the smaller the particle size of the mercury-containing sediment, the higher the migration speed as well as the more comprehensive migration range. From the numerical simulation results, it was found that mercury was mainly distributed in the southwest and northeast directions from Minamata Bay. Finally, the simulated mercury distribution, which considers the relationship between particle size and mercury concentration, shows a high agreement with the past measurements of mercury, suggesting the importance of particle size effect in mercury migration.