Nitrogen and iron largely determine phytoplankton production in the ocean, yet there are few direct incubation studies on nutrient limitation of phytoplankton in the western tropical North Pacific Ocean. Here, we assessed the effects of N and Fe amendments on both photosynthesis and biomass of phytoplankton (including final chlorophyll a biomass and taxonomic composition) in that region. Overall, the carrying capacity of phytoplankton biomass was primarily constrained by N, and Fe was a limiting resource only near the equator where phytoplankton was co-limited by N and Fe. Positive growth responses in nutrient-receiving treatments were predominantly caused by diatoms, sometimes together with Synechococcus. The often strong stimulation of large phytoplankton in these treatments substantially modified the phytoplankton assemblage from picoplankton-to diatom-dominated, which was often accompanied by a significant increase in photosynthetic competence. This is the first report showing that phytoplankton in the tropical western North Pacific are primarily limited by N, and co-limited by Fe in some areas. We combined our results with those from comparable studies in the tropical and subtropical Pacific Ocean to propose a general typology that describes and predicts the long-term effects of rate-limiting N and Fe on phytoplankton final biomass and changes in community structure.