Abstract: Passive containment cooling system, as one of advanced safety features employed in HPR1000, is a natural circulation system. Since the cooling capacity is highly depended on water temperature in water storage tank, thermal stratification phenomena in water storage tank should be well evaluated and the investigation is also meaningful for engineering design optimization. A transient simulation of heating process on the water storage tank with 3D model was conducted by CFD method in the paper. The results show that thermal stratification occurs in the water storage tank, and the temperature at the top of the pool fluctuates greatly, while at the bottom goes mildly. Both circulation flow rate and power impact temperature increase of water body and thermal stratification in the water storage tank. Higher power and/or fewer flow rate promote thermal stratification and make water temperature in tank and on outlet of system higher. Two trains of cooling systems which run under different conditions have rare impact on formation of thermal stratification in the water storage tank and characteristic temperatures like average temperature and outlet-temperature, which indicates that the water storage tank has self-stability on circulation of passive cooling system.