The heat storage technology can improve the performance of a solar thermal utilization system effectively. This work studied the effect of phase-change materials (PCMs) on thermal stratification in a heat storage tank. A 60 l sodium acetate trihydrate heat storage tank with 331.15 K phase-change temperature was designed and fabricated. A mathematical model was built to simulate the discharge process in the water tank, and the temperature distribution during the discharge process was obtained. The computational fluid dynamics model was verified by the experimental data. Furthermore, the Ri, the fill efficiency, and the MIX number were adopted to extensively analyze the performance of a heat storage tank with different positions of PCMs with the variation of flow rates. The results indicated that the distance between the isothermal surfaces of 303.15 K and 348.15 K in PCM1, PCM2, PCM3, and PCM4 were 11.75 cm, 11.13 cm, 10.52 cm, and 9.28 cm, respectively, with 9 l/min of flow velocity when t* = 0.7, showing that the thermal stratification was improved as the position of the PCMs got closer to the inlet. The PCMs’ half-life (the liquefaction rate reached 50%) was prolonged as the inlet flow rates increased. As the flow rate increased from 1 l/min to 5 l/min, the half-life of PCM4 delayed from a dimensionless time of 0.5 to a dimensionless time of 0.9. Moreover, when the flow velocity was 9 L/min, the liquefaction rate of PCM4 remained at 1. The calculated values of fill efficiency and Richardson number were higher than the experimental data slightly, while the MIX number was smaller than the experimental results. The experimental and calculated values of root mean square error (RMSE) increased with the increasing inlet flow velocity and the lowering of the positions of the PCMs.