In order to improve the accuracy of internal temperature estimation in batteries, a 10-parameter time-varying multi-surface heat transfer model including internal heat production, heat transfer and external heat transfer is established based on the structure of a lithium iron phosphate pouch battery and its three directional anisotropic heat conduction characteristics. The entropy heat coefficient, internal equivalent heat capacity and internal equivalent thermal resistance related to the SOC and temperature state of the battery were identified using experimental tests and the least square fitting method, and were then used for online calculation of internal heat production and heat transfer in the battery. According to the time-varying and nonlinear characteristics of the heat transfer between the surface and the environment of the battery, an internal temperature estimation algorithm based on the square root cubature Kalman filter was designed and developed. By iteratively calculating the estimated surface temperature and the measured value, dynamic tracking and online correction of the internal temperature of the battery can be achieved. The verification results using FUDS and US06 dynamic working condition data show that the proposed method can quickly eliminate the influence of initial temperature deviations and accumulated process errors and has the characteristics of a high estimation accuracy and good robustness. Compared with the estimation results of the adaptive Kalman filter, the proposed method improves the estimation accuracy of FUDS and US06 working conditions by 67% and 54%, respectively, with a similar computational efficiency.