This paper presents a real-time estimation method for the temperature distribution of cylindrical batteries under boundary air cooling. A space-/time-separation-based analytical model is developed using Karhunen–Loève decomposition and Galerkin's method. The model parameters can be identified and optimized using data-based approaches. The developed analytical model demonstrates the robustness to variation of thermal parameters. However, the change of boundary cooling will significantly degrade the performance of the developed analytical model. For the known boundary cooling, the compensation model for cooling effects can be derived to improve the modeling performance. For the unknown boundary cooling in real practice, a dual-extended Kalman filter can be used to simultaneously estimate coupled parameters and convection coefficient in the compensation model. The proposed method can achieve satisfactory performance in the battery duty-cycle experiments.