Due to the sensitivity of the electrochemical performance of lithium-ion batteries to temperature, the thermal management system becomes an essential component of pure electric vehicles. This paper selects a liquid-cooled double-layer battery pack for a certain car as the research object, determines the heating power of the battery cell through experiments, considers the existence of air domain in the battery pack to establish a battery pack thermal management system model, and analyzes the effects of different discharge rates, inlet flow rates, and inlet flow directions on the thermal performance of the double-layer battery pack. The results show that the temperature of the upper module of the double-layer battery pack is higher than that of the lower module at the same discharge rates and inlet flow rate; the maximum temperature of the upper module can be effectively reduced by increasing the liquid intake flow of the upper module. When the inlet flow rate of the upper module and the lower module is 550 and 500 L/hour respectively, the temperature distribution difference between the upper and lower modules of the double-layer battery pack is the smallest, and the heat dissipation performance of the battery pack is the better. The conclusion can provide reference for structural design and optimization of thermal management system of the liquid-cooled double-layer battery pack.