The Northwest Pacific Ocean encompasses complex current structures and mesoscale warm and cold eddies. Due to the unique physical processes of mesoscale eddies, the chemical properties and biological composition are distinct. Phytoplankton account for roughly half of global net primary production and play an essential role in marine ecosystems. High-resolution horizontal and vertical investigations and remote sensing data are required to clarify the processes and mechanisms associated with these complex changes. This study investigated phytoplankton community structure in the Northwest Pacific Ocean in 2018 and revealed the spatial variability of phytoplankton in community composition and abundance. In addition, the relationship of distribution of phytoplankton and mesoscale physical processes were analyzed. In the affected area of Mindanao eddy (ME), the high value of TChl a was observerd in the 50m layer. Pico-phytoplankton was the dominant group in the areas, mainly Prochlorococcus, followed by haptophytes-8. Diatoms and dinoflagellates contributed less than 10% to the biomass of the phytoplankton. However, Diatoms increased significantly at the 50 m layer in the low-latitude area under the influence of the ME. The main environmental factors affecting the distribution of phytoplankton were SSH and temperature. Overall, our study revealed changes in the phytoplankton communities during the different currents and eddies.