Thermal management is a routine but crucial strategy to ensure thermal stability and long-term durability of the lithium-ion batteries. An air-flow-integrated thermal management system is designed in the present study to dissipate heat generation and uniformize the distribution of temperature in the lithium-ion batteries. The system contains of two types of air ducts with independent intake channels and fans. One is to cool the batteries through the regular channel, and the other minimizes the heat accumulations in the middle pack of batteries through jet cooling. A three-dimensional anisotropic heat transfer model is developed to describe the thermal behavior of the lithium-ion batteries with the integration of heat generation theory, and validated through both simulations and experiments. Moreover, the simulations and experiments show that the maximum temperature can be decreased to 33.1 °C through the new thermal management system in comparison with 42.3 °C through the traditional ones, and temperature uniformity of the lithium-ion battery packs is enhanced, significantly.