Community structure of heterotrophic protists and their grazing impact on phytoplankton were studied in Northwest Pacific Ocean during October, 2007. The study area was divided into four regions based on physical properties (temperature and salinity) and chlorophyll-a distribution. They were Region I of North Equatorial Currents, Region II of Kuroshio waters, Region III of shelf mixed water, and Region IV of Tsushima warm current from East China Sea. The distribution of chlorophyll-a concentrations and community structure of heterotrophic protists were significantly affected by physical properties of the water column. The lowest concentration of chlorophyll-a was identified in Region I and II, where pico-sized chlorophyll-a was most dominant (>80% of total chlorophyll-a). Biomass of heterotrophic protists was also low in Region I and II. However, Region III was characterized by low salinity and temperature and high chlorophyll-a concentration, with relatively lower pico-sized chlorophyll-a dominance. The Highest biomass of heterotrophic protists appeared in Region III, along with the relatively less important nanoprotists. In Region I, II and IV, heterotrophic dinoflagellates were dominant among the protists, while ciliates were dominant in Region III. Community structure varied with physical(salinity and temperature) and biological (chlorophyll-a) properties. Biomass of heterotrophic protists correlated well with chlorophyll-a concentration in the study area ($r^2=0.66$, p<0.0001). The potential effect of grazing activity on phytoplankton is relatively high in Region I and II. Our result suggest that biomass and size structure of heterotrophic protists might be significantly influenced by phytoplankton size and concentration.