For the problems such as high uncertainty in assembly accuracy transmission and post-assembly forced alignment by the current assembly coordination methods that are mainly based on geometric quantity control, this study investigates the cumulative transmission mechanism and quantitative evaluation methods of assembly coordination errors that incorporate the practical error state. Firstly, the deformation during the assembly process of aeronautical thinwalled parts was analyzed, and an error transmission path model for flexible assemblies was constructed based on the symbolic matrix of flexible mating surfaces. Secondly, based on the small displacement torsor theory and homogeneous transformation theory, an initial deviation transmission calculation matrix was constructed. By obtaining the multi-physical field coupling deviation in real-time, the deviation transmission factors were dynamically updated during the assembly process and the transmission calculation matrix w as corrected to accurately calculate the assembly error. Furthermore, with the help of the stability entropy function, a comprehensive evaluation system was established with the assembly error value as the leading indicator, and the local entropy value as the additional indicator, and the accurate evaluation of the cumulative error state on the thin-wall surface could be achieved. Finally, a wing-box structure was taken as an example for verification, and the improvement of the assembly quality was achieved significantly.