Flexible flow-shop scheduling with dynamic transport waiting times (FFSPDW) is a typical flow shop scheduling problem in smart manufacturing system. In this problem, jobs need to be transported by transporters like AGV (Automated Guided Vehicle) to next stage after processing. During transportation, waiting time dynamically occurs for both jobs and transporters, and finally contributes to makespan. The waiting times are conditioned by buffer capacity, machine allocations and production sequence. In order to minimize makespan with consideration of dynamic waiting times, we proposed a waiting time calculation approach to evaluate waiting time and makespan. This approach considers two situations: infinite buffer capacity and zero buffer capacity. Further, we developed a memetic algorithm integrated with waiting time calculation approach to solve FFSPDW. Finally, we verified the algorithm parameters via analysis of variance. Computational results show that the proposed memetic algorithm is able to reach high quality solutions with short computation time. Consequently, the proposed approach is suitable for solving industrial FFSPDW problems.