We developed a global three-dimensional physical–biological coupled model and applied it in simulations with and without ontogenetic seasonal vertical migration of large zooplankton (copepods). The annual cycle of phytoplankton behaviour is well reproduced by this model with the seasonal vertical migration of zooplankton. A comparison of the two cases shows that in the northwestern Pacific and subarctic southern ocean, primary production is higher in the case with vertical migration. In these regions, large phytoplankton (diatoms) dominate, and the presence of large zooplankton throughout the year reduces primary production by large phytoplankton (diatoms). This effect is greatest for the diatom bloom. On the other hand, for regions where small phytoplankton dominate, primary production is higher in the case without vertical migration. This is because small zooplankton are suppressed by grazing pressure from large zooplankton, reducing grazing pressure on small phytoplankton.