With the engineering background of Urumqi region’s solar water heating system for floor heating, this paper analyzed the fluid flow and heat transfer processes inside three thermal storage tanks with different top or obstacle structures numerically in order to make full use of solar energy and improve the comprehensive efficiency of solar energy system. The alternate operation mode of each water tank is also discussed. The results show that it is feasible to use the multi-tank alternate operation mode at different times. According to the thermal stratification evaluation results of the water tank, at three typical moments(11:30, 15:00 and 18:00) when the outdoor temperature during the typical day is relatively stable in the region, the reasonable operation mode of the water tank is: at 11:30, 3# water tank (spherical top and obstacle inside the tank with single round hole) is preferentially operated, followed by 2# water tank (conical top and obstacle inside the tank with five round holes) or 1# water tank (conical top and obstacle inside the tank with single round hole); at 15:00 and 18:00, 3# water tank should be preferentially operated while 1# and 2# water tanks can be used as backup for each other. For users with higher water temperature requirements but less water consumption, it is suggested that 3# water tank is preferentially operated, followed by the 1# water tank. When users generate a lot of backwater and need hot water with higher temperature, the operation of 2# water tank is preferred. It is of great engineering guiding significance to operate appropriate hot water storage tank in a timely manner and adjust the fluid parameters according to the local meteorological conditions so as to make full use of solar energy resources and improve the reliability of the solar heating system.