Various modeling studies have examined the climatic effects of either the Central American Seaway or the Indonesian seaway. The co-existence of these two tropical seaways may have a greater influence than the existence of a single seaway. Although the dual seaway situation is closer to that reconstructed during Miocene/Pliocene, relevant studies remain scarce. Here, we investigate the co-effects of dual tropical seaway changes on the Pacific circulation through a set of sensitivity experiments. Our results show that the combined shallow opening of tropical seaways can generate an active Pacific meridional overturning circulation and maintain strong upwelling conditions along the equatorial Pacific, which may have helped favor a “biogenic bloom” during the late Miocene and early Pliocene. Moreover, the logically successive closure of the tropical seaways can provide patterns of zonal sea surface temperature gradients that are similar to those recorded in the equatorial Pacific from the late Miocene to the Pliocene.