The distributed assembly mixed no-idle permutation flowshop scheduling problem (DAMNIPFSP), a common occurrence in modern industries like integrated circuit production, ceramic frit production, fiberglass processing, and steel-making, is a new model that considers mixed machines with no-idle restrictions as well as conventional machines. This article introduces an estimation of distribution algorithm-based hyper-heuristic (EDA-HH) to solve the DAMNIPFSP. Ten simple heuristic rules as low-level operations are utilized to search the solution space. The estimation of distribution algorithm is integrated into the framework of hyper-heuristic as the high-level strategy to control the low-level heuristics sequence in the solution space. The destruction and construction procedures are conducted on products and jobs in order to enhance the exploitation competence of EDA-HH. The computational simulation is carried out and the experimental results show that the proposed EDA-HH is significantly superior to the competitors in the statistical sense. The results of the 810 large-scale problem instances show the effectiveness of the EDA-HH in solving the DAMNIPFSP. Moreover, the CPLEX solver is utilized to verify the correctness of the model with some small instances.