Abstract. Vertical stratification determined the variability of temperature and nutrient distribution in upper seawater, thereby affecting the primary production of the ocean. Nutrients in the oligo-trophic region vary in time and space, and thus phytoplankton vary in their vertical distribution. However, the differences in the vertical distribution of phytoplankton have not been systematically studied. This study investigated the spatial distribution pattern and diversity of phytoplankton communities in the western Pacific Ocean (WPO) in the autumn of 2016, 2017 and 2018, as well as the local hydrological and nutritional status. The Utermöhl method was used to analyze the relevant ecological characteristics of phytoplankton in the surveyed sea area. In the three cruises investigated, we show universal relationships between phytoplankton and (1) vertical stratification, (2) N : P ratio (3) temperature and salinity. The potential influencing factors of physical and chemical parameters on phytoplankton abundance were analyzed by structural equation model (SEM), determining the vertical stratification index was the most important influence factor affecting phytoplankton abundance and indirectly on phytoplankton abundance by dissolved inorganic nitrogen (DIN) and Dissolved inorganic phosphorus (DIP). Vertical stratification determines the vertical distribution of the phytoplankton community structure in the WPO. The areas with strong vertical stratification (Group A and B) are more conducive to the growth of cyanobacteria, and the areas with weak vertical stratification (Group C and D) are more conducive to the bloom of diatoms and dinoflagellates.