During the late Miocene and the Pliocene, changes in the Central American and the Indonesian seaways geometry are very important for ocean circulation and global climate. Various modelling studies have examined the separate effects of these two tropical seaways, especially their link to the onset of the Northern Hemisphere ice sheets through changes in the Atlantic meridional overturning circulation and associated heat and moisture transport. Although the existence of dual tropical seaways is closer to the reality, there are very scarce modelling studies exploring the co-effects of dual tropical seaway changes, especially on the Pacific ocean circulation. Here we provide the results of modelling study on this issue. Our results show that the combined shallow opening of tropical ways can generate an active Pacific meridional overturning circulation (that is absent in modern conditions) by which the meridional and zonal sea surface temperature gradient in the Pacific largely reduce. In contrast, a deeper opening of tropical seaways cannot produce these changes in the Pacific ocean circulation. This study provides insights into and a better understanding of the role of tropical seaways in shaping the Pacific climate and highlights the importance of the sill depth of each seaway.