In this paper, an effective Hyper Heuristic-based Memetic Algorithm (HHMA) is proposed to solve the Distributed Assembly Permutation Flow-shop Scheduling Problem (DAPFSP) with the objective of minimizing the maximum completion time. A novel searching-stage-based solution representation scheme is presented for both improving the search efficiency and maintaining potential solutions. In the global search stage, Estimation of Distribution Algorithm (EDA) is employed as the high level strategy of EDA-based Hyper Heuristic (EDAHH) to find promising product sequences for further exploitation. Based on the newly found knowledge of critical-products, several efficient Low-Level Heuristics (LLHs) are well designed to construct the LLH set so that the powerful exploration ability of the EDAHH can be guaranteed. A simulated-annealing-like type of acceptance criterion is also embedded into each LLH to avoid premature convergence. Then a Critical-Products-based Referenced Local Search (CP-RLS) method is proposed to improve the quality of superior sub-population by operating on the sub-job-sequences derived from the critical products. The benefit of the presented CP-RLS lies in the excellent exploitation ability with substantially reduced computational cost. Finally, performance evaluation and comparison are both carried out on a benchmark set and the results demonstrate the superiority of HHMA over the state-of-the-art algorithms for the DAPFSP.