At present, discrete workshops demand higher transportation efficiency, but the traditional scheduling strategy of the logistics systems can no longer meet the requirements. In a transportation system with multiple automated guided vehicles (multi-AGVs), AGV path conflicts directly affect the efficiency and coordination of the whole system. At the same time, the uncertainty of the number and speed of AGVs will lead to excessive cost. To solve these problems, an AGVs Multi-Objective Dynamic Scheduling (AMODS) method is proposed which is based on the digital twin of the workshop. The digital twin of the workshop is built in the virtual space, and a two-way exchange and real-time control framework based on dynamic data is established. The digital twin system is adopted to exchange data in real time, create a real-time updated dynamic task list, determine the number of AGVs and the speed of AGVs under different working conditions, and effectively improve the efficiency of the logistics system. Compared with the traditional scheduling strategy, this paper is of practical significance for the scheduling of the discrete workshop logistics systems to improve the production efficiency, utilization rate of resources, and dynamic response capability.