For ensuring the safety of lithium-ion batteries in application, keeping the temperature of the battery pack in the desired range is crucial under different operating condition. This paper incorporates experiments and the numerical model to design a novel thermal management system with the combination of the phase change material and liquid cooling for twelve cylindrical lithium-ion batteries. The experimental results reveal that at the ambient temperature of 35 °C, the maximum temperature and temperature difference of the blank control system during 1 C charge and 2 C discharge are 57.6 °C and 4.1 °C, while the maximum temperature difference is 3.6 °C with single liquid cooling. Compared with them, the maximum temperature of the coupled system is only 44.8 °C and the maximum temperature difference is less than 2 °C with superior cycling performance. Moreover, an electric-thermal model is proposed to study the cooling effect of coolant, from which controlling the coolant flow within 250 mL/min is the best choice. Based on these results, an optimization strategy of hierarchical management is proposed for the coolant flow and inlet temperature by monitoring the maximum temperature of the battery pack and ambient temperature. This strategy not only controls the temperature of the system in desired range under different ambient temperatures, but also reduces the unnecessary energy consumption of liquid cooling. The proposed system is scalable to be applied to the other types of batteries for thermal management.