The invention discloses a flexible intelligent manufacturing system for hybrid multi-workpiece processing. The system comprises a central platform, wherein the central platform is connected with a network control system through a power supply wire, the network control system comprises an operation system and a database management system, the operation system is connected with an FMS operation control system through a power supply wire, the database management system is connected with a transmission module through a power supply wire, the transmission module is connected with a data storage module through a power supply wire, and the FMS operation control system comprises a production preparation system, a material management control system, a dynamic scheduling system and a real-time faultdiagnosis system. The flexible intelligent manufacturing system is advantaged in that productivity is high, the equipment is fixed, the equipment utilization rate for flexible manufacturing is further high, cost of single products is low, one or several similar parts can be processed, production of many varieties of small and medium batches can be carried out, efficiency of hybrid workpiece processing is improved, and labor intensity of operators is reduced.