The North Equatorial Current (NEC) is an essential part of the global warm pool and plays a key role in the subtropical and tropical circulation systems of the North Pacific. As the current is transported from east to west, significant changes in the structure and function of the associated ecosystem are expected. However, the complexity of the current systems and the region's remote location far from the continent have resulted in limited observational data, leaving biogeographic distributions, phytoplankton diversity, and their driving mechanisms poorly understood. To bridge this gap, we used a multidisciplinary approach of field and satellite observations, reanalysis data, and BGC-Argo data to gain a more comprehensive understanding of the NEC. The results revealed that the biogeochemical characteristics of the NEC were regulated by seasonal variations and also exhibited spatial differences. The diversity of phytoplankton communities was primarily controlled by the NEC transport but was additionally influenced by mesoscale eddies. Chlorophyll a concentrations in the NEC decreased from east to west but increased again near the Mindanao Eddy. The Shannon-Wiener diversity index was lowest on the western side of the NEC, showing significant differences compared to the other stations. Our findings suggested that ocean currents, in conjunction with mesoscale eddies, acted as both transport pathways and diffusion barriers, thereby influencing phytoplankton diversity. This study provided essential reference data for the future conservation of marine ecosystems and fishery resources in the northwestern Pacific.