An electric motor assembly flowshop (EMAF) is a type of classical mixed-product assembly line that uses automatic guided vehicle (AGV) systems for material handling. To optimise the logistics system configuration and alleviate the impact of the AGV parameters on the efficiency of the EMAF, a modelling and optimisation method based on discrete event simulation (DES) combined with Taguchi orthogonal experimental design was proposed. A DES model of the entire production process for the EMAF was constructed using the Tecnomatix Plant Simulation software package. After optimisation of the principal layout in the DES model, the number of assembly stations was decreased from 13 to 9, and the balance ratio was increased from 65.08% to 84.65%. In addition, the combination of the Taguchi method with the DES model was further developed to achieve the optimal parameter combination of the AGVs in order to allow the AGVs to operate more efficiently under various states. The final overall theoretical throughput was increased from 134 to 295 units within the seven-hour observation period.