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This study explores the influence of Stokes drift and the thermal effects on the upper ocean bias which occurs inthe summer with overestimated sea surface temperature (SST) and shallower mixed layer depth (MLD) using Mellor-Yamada turbulence closure scheme. The upper ocean thermal structures through Princeton ocean model are examined by experiments in the cases of idealized forcing and real observational situation. The results suggest that Stokes drift can generally enhance turbulence kinetic energy and deepen MLD either in summer or in winter. This effect will improve the simulation results in summer, but it will lead to much deeper MLD in winter compared to observational data. It is found that MLD can be correctly simulated by combining Stokes drift and the thermal effects of the cool skin layer and dial warm layer on the upper mixing layer. In the case of high shortwave radiation and weak wind speed, which usually occurs in summer, the heat absorbed from sun is blocked in the warm layer and prevented from being transferred downwards. As a result, the thermal effects in summer nearly has no influence on dynamic effect of Stokes drift that leads to deepening MLD. However, when the stratification is weak in winter, the thermal effects will counteract the dynamic effect of Stokes drift through enhancing the strength of stratification and suppress mixing impact. Therefore, the dynamic and thermal effects should be considered simultaneously in order to correctly simulate upper ocean thermal structures in both summer and winter.