Base on the Hybrid Coordinate Ocean Model (HYCOM), this paper simulated the three dimensional dynamic and thermologic structure of the North Pacific Ocean from 1981 to 2001. After verifying the validation of the model results, the mixed layer depth (MLD) field and its seasonal variation in Japan/East Sea (JES) as well as the interannual variation were analyzed. The analysis shows that there exists strong seasonal and interannual variations of MLD in JES; which can be seen as one of the noticeable hydrological phenomena there. The MLD is deeper in winter and shallower in summer. The variable range is from 10 meters to 100 meters. There exists both similarity and difference between seasonal and interannual variations of MLD in JES. The analysis shows that the topography, the current, the monsoon and the temperature gradient in JES work together, making the variation of MLD in JES.