Nowadays, the focus of flow shops is the adoption of customized demand in the context of service-oriented manufacturing. Since production tasks are often characterized by multi-variety, low volume, and a short lead time, it becomes an indispensable factor to include supporting logistics in practical scheduling decisions to reflect the frequent transport of jobs between resources. Motivated by the above background, a hybrid method based on dual back propagation (BP) neural networks is proposed to meet the real-time scheduling requirements with the aim of integrating production and transport activities. First, according to different resource attributes, the hierarchical structure of a flow shop is divided into three layers, respectively: the operation task layer, the job logistics layer, and the production resource layer. Based on the process logic relationships between intra-layer and inter-layer elements, an operation task–logistics–resource supernetwork model is established. Secondly, a dual BP neural network scheduling algorithm is designed for determining an operations sequence involving the transport time. The neural network 1 is used for the initial classification of operation tasks’ priority; and the neural network 2 is used for the sorting of conflicting tasks in the same priority, which can effectively reduce the amount of computational time and dramatically accelerate the solution speed. Finally, the effectiveness of the proposed method is verified by comparing the completion time and computational time for different examples. The numerical simulation results show that with the increase in problem scale, the solution ability of the traditional method gradually deteriorates, while the dual BP neural network has a stable performance and fast computational time.