This paper proposes a novel distributed assembly flexible job shop scheduling problem (DAFJSP), which involves three stages: production stage, assembly stage, and delivery stage. The production stage is accomplished in a few flexible job shops, the assembly stage is accomplished in a few single-machine factories, and the delivery stage is to deliver the obtained products to the corresponding customers. To address the problem, a hybrid estimation of distribution algorithm based on differential evolution operator and variable neighborhood search (HEDA-DEV) is proposed with the goal of minimizing the total cost and tardiness. Firstly, a new multidimensional coding method is designed based on the features of the DAFJSP. Secondly, two mutation operators and the similarity coefficient based on the probability matrix are put forward to implement the dynamic mutation. Thirdly, five types of neighborhood structures satisfying cooperative search strategies are employed to adequately improve the local exploitation ability. Finally, the comparison experiment results suggest that the proposed HEDA-DEV has competitive performance compared to the selected efficient algorithms. Moreover, a real case study is used to demonstrate that HEDA-DEV is an effective method for solving DAFJSP.