There are many deviation sources in the assembly process of aircraft complex thin-walled structures. To get important factors that affect quality, it is crucial to diagnose the key deviation resources. The deviation transfer between deviation sources and assembly parts has the characteristics of small sample size, nonlinearity, and strong coupling, so it is difficult to diagnose the key deviation sources by constructing assembly dimension chains. Therefore, based on the deviation detection data, transfer entropy and complex network theory are introduced. Integrating the depth-first traversal algorithm with degree centrality theory, a key deviation diagnosis method for complex thin-walled structures is proposed based on weighted transfer entropy and complex networks. The application shows that key deviation sources that affect assembly quality can be accurately identified by the key deviation source diagnosis method based on complex networks and weighted transfer entropy.