The current literature mainly uses hub capacity or transport route selection to manage the congestion of emergency multimodal transport and pays less attention to transshipment scheduling. This paper proposes an integrated optimization problem of transport routes and transshipment sequences (ITRTSP) and constructs a hybrid flow shop scheduling model to describe it. Based on this model, a recursive method is proposed to calculate the minimum waiting times that cargoes consume in queues at hubs, given the transport routes and transshipment sequences. Furthermore, a memetic algorithm is designed with route selection as the outer layer and transshipment sequence selection as the inner layer for solving ITRTSP. Compared with existing achievements, the model and algorithms can quantify the dependency between transshipment sequence selection and emergency transport time in multimodal transport network settings. The model and algorithms are applied to solve some real-scale examples and compared with the first-come-first-served (FCFS) rule commonly used in the current literature. The results indicate that the makespan is reduced by up to approximately 4.2%, saving 33.68 h. These findings demonstrate that even with given hub capacities and transport routes, congestion can still be managed and the schedule optimized through transshipment scheduling, further improving emergency transport efficiency.