Seasonal variation of phytoplankton was investigated with surface mixed layer ecosystem model in the East Sea. The model consisted of four compartments (phytoplankton, zooplankton, nutrient, detritus) forced by mixed layer depths, photosynthetically available radiation and nutrient concentrations. From model results we estimated entrainment rate $2.5-4.0;m{cdot}day^{-1}$ to reproduce the two annual blooms, and reproduced seasonal variation of phytoplankton at southern and northern regions by the difference of surface winter mixed layer depth (MLD) using the entrainment rate value $3.0;m{cdot}day^{-1}$. The spring blooms in the southern and northern regions closely related to deepening of a winter surface MLD. In the southern region where MLD was shallow and phytoplankton spring bloom occurs one month in advance to the northern region where MLD was deep. The amount of light increases within the MLD during the onset of stratification and water temperature increases faster in spring in the southern region than the northern region. Decrease of phytoplankton was mainly affected by zooplankton grazing in the southern region and by nutrient exhaustion in the northern region. The fall bloom in the two regions was caused by the nutrient availability and entrainment on the phytoplankton.